diff --git a/pkgs/applications/misc/octoprint/default.nix b/pkgs/applications/misc/octoprint/default.nix
index 99d23b0eb7c..41bc94a5130 100644
--- a/pkgs/applications/misc/octoprint/default.nix
+++ b/pkgs/applications/misc/octoprint/default.nix
@@ -62,6 +62,14 @@ let
         # No tests included
         doCheck = false;
       };
+
+      pylru = super.pylru.overridePythonAttrs (oldAttrs: rec {
+        version = "1.0.9";
+        src = oldAttrs.src.override {
+          inherit version;
+          sha256 = "71376192671f0ad1690b2a7427d39a29b1df994c8469a9b46b03ed7e28c0172c";
+        };
+      });
     };
   };
 
diff --git a/pkgs/applications/networking/newsreaders/pan/default.nix b/pkgs/applications/networking/newsreaders/pan/default.nix
index 4a1940ae654..9d51a76f536 100644
--- a/pkgs/applications/networking/newsreaders/pan/default.nix
+++ b/pkgs/applications/networking/newsreaders/pan/default.nix
@@ -2,7 +2,7 @@
 , stdenv, fetchurl, pkgconfig, gtk3, gtkspell3 ? null
 , perl, gmime2, gettext, intltool, itstool, libxml2, dbus-glib, libnotify, gnutls
 , makeWrapper, gnupg
-, gnomeSupport ? true, libgnome-keyring3
+, gnomeSupport ? true, gnome3, libsecret
 }:
 
 assert spellChecking -> gtkspell3 != null;
@@ -17,10 +17,10 @@ stdenv.mkDerivation {
     sha256 = "1b4wamv33hprghcjk903bpvnd233yxyrm18qnh13alc8h1553nk8";
   };
 
-  nativeBuildInputs = [ pkgconfig makeWrapper ];
-  buildInputs = [ gtk3 perl gmime2 gettext intltool itstool libxml2 dbus-glib libnotify gnutls ]
+  nativeBuildInputs = [ pkgconfig gettext intltool itstool libxml2 makeWrapper ];
+  buildInputs = [ gtk3 gmime2 libnotify gnutls ]
     ++ stdenv.lib.optional spellChecking gtkspell3
-    ++ stdenv.lib.optional gnomeSupport libgnome-keyring3;
+    ++ stdenv.lib.optionals gnomeSupport [ libsecret gnome3.gcr ];
 
   configureFlags = [
     "--with-dbus"
diff --git a/pkgs/applications/science/math/sage/default.nix b/pkgs/applications/science/math/sage/default.nix
index 7e62f0cf75e..08e3a752b8b 100644
--- a/pkgs/applications/science/math/sage/default.nix
+++ b/pkgs/applications/science/math/sage/default.nix
@@ -21,7 +21,7 @@ let
 
       sagelib = self.callPackage ./sagelib.nix {
         inherit flint ecl arb;
-        inherit sage-src openblas-blas-pc openblas-cblas-pc openblas-lapack-pc pynac singular;
+        inherit sage-src pynac singular;
         linbox = nixpkgs.linbox.override { withSage = true; };
       };
 
@@ -41,13 +41,13 @@ let
       };
 
       sage-env = self.callPackage ./sage-env.nix {
-        inherit sage-src python rWrapper openblas-cblas-pc ecl singular palp flint pynac pythonEnv;
+        inherit sage-src python rWrapper ecl singular palp flint pynac pythonEnv;
         pkg-config = nixpkgs.pkgconfig; # not to confuse with pythonPackages.pkgconfig
       };
 
       sage-with-env = self.callPackage ./sage-with-env.nix {
         inherit pythonEnv;
-        inherit sage-src openblas-blas-pc openblas-cblas-pc openblas-lapack-pc pynac singular;
+        inherit sage-src pynac singular;
         pkg-config = nixpkgs.pkgconfig; # not to confuse with pythonPackages.pkgconfig
         three = nodePackages_8_x.three;
       };
@@ -60,10 +60,6 @@ let
     };
   };
 
-  openblas-blas-pc = callPackage ./openblas-pc.nix { name = "blas"; };
-  openblas-cblas-pc = callPackage ./openblas-pc.nix { name = "cblas"; };
-  openblas-lapack-pc = callPackage ./openblas-pc.nix { name = "lapack"; };
-
   sage-src = callPackage ./sage-src.nix {};
 
   pythonRuntimeDeps = with python.pkgs; [
diff --git a/pkgs/applications/science/math/sage/openblas-pc.nix b/pkgs/applications/science/math/sage/openblas-pc.nix
deleted file mode 100644
index f4669a6557e..00000000000
--- a/pkgs/applications/science/math/sage/openblas-pc.nix
+++ /dev/null
@@ -1,17 +0,0 @@
-{ openblasCompat
-, writeTextFile
-, name
-}:
-
-writeTextFile {
-  name = "openblas-${name}-pc-${openblasCompat.version}";
-  destination = "/lib/pkgconfig/${name}.pc";
-  text = ''
-    Name: ${name}
-    Version: ${openblasCompat.version}
-
-    Description: ${name} for SageMath, provided by the OpenBLAS package.
-    Cflags: -I${openblasCompat}/include
-    Libs: -L${openblasCompat}/lib -lopenblas
-  '';
-}
diff --git a/pkgs/applications/science/math/sage/sage-env.nix b/pkgs/applications/science/math/sage/sage-env.nix
index 317eb6e16c4..74c2e0aa036 100644
--- a/pkgs/applications/science/math/sage/sage-env.nix
+++ b/pkgs/applications/science/math/sage/sage-env.nix
@@ -37,7 +37,7 @@
 , lcalc
 , rubiks
 , flintqs
-, openblas-cblas-pc
+, openblasCompat
 , flint
 , gmp
 , mpfr
@@ -98,9 +98,9 @@ writeTextFile rec {
     export PKG_CONFIG_PATH='${lib.concatStringsSep ":" (map (pkg: "${pkg}/lib/pkgconfig") [
         # This is only needed in the src/sage/misc/cython.py test and I'm not sure if there's really a use-case
         # for it outside of the tests. However since singular and openblas are runtime dependencies anyways
-        # and openblas-cblas-pc is tiny, it doesn't really hurt to include.
+        # it doesn't really hurt to include.
         singular
-        openblas-cblas-pc
+        openblasCompat
       ])
     }'
     export SAGE_ROOT='${sage-src}'
diff --git a/pkgs/applications/science/math/sage/sage-with-env.nix b/pkgs/applications/science/math/sage/sage-with-env.nix
index 63b9772b823..8ccf8b5a493 100644
--- a/pkgs/applications/science/math/sage/sage-with-env.nix
+++ b/pkgs/applications/science/math/sage/sage-with-env.nix
@@ -4,9 +4,6 @@
 , sage-env
 , sage-src
 , openblasCompat
-, openblas-blas-pc
-, openblas-cblas-pc
-, openblas-lapack-pc
 , pkg-config
 , three
 , singular
@@ -32,9 +29,6 @@ let
     makeWrapper
     pkg-config
     openblasCompat # lots of segfaults with regular (64 bit) openblas
-    openblas-blas-pc
-    openblas-cblas-pc
-    openblas-lapack-pc
     singular
     three
     pynac
diff --git a/pkgs/applications/science/math/sage/sagelib.nix b/pkgs/applications/science/math/sage/sagelib.nix
index abcefba5e26..c1dbcf38304 100644
--- a/pkgs/applications/science/math/sage/sagelib.nix
+++ b/pkgs/applications/science/math/sage/sagelib.nix
@@ -3,9 +3,6 @@
 , buildPythonPackage
 , arb
 , openblasCompat
-, openblas-blas-pc
-, openblas-cblas-pc
-, openblas-lapack-pc
 , brial
 , cliquer
 , cypari2
@@ -59,9 +56,7 @@ buildPythonPackage rec {
   nativeBuildInputs = [
     iml
     perl
-    openblas-blas-pc
-    openblas-cblas-pc
-    openblas-lapack-pc
+    openblasCompat
     jupyter_core
   ];
 
diff --git a/pkgs/applications/science/molecular-dynamics/lammps/default.nix b/pkgs/applications/science/molecular-dynamics/lammps/default.nix
index 9a89b88d7a5..03e37ad9d93 100644
--- a/pkgs/applications/science/molecular-dynamics/lammps/default.nix
+++ b/pkgs/applications/science/molecular-dynamics/lammps/default.nix
@@ -1,25 +1,37 @@
-{ stdenv, writeText, fetchurl,
-  libpng, fftw,
-  mpiSupport ? false, mpi ? null
+{ lib
+, bash
+, stdenv
+, writeText
+, fetchFromGitHub
+, libpng
+, gzip
+, fftw
+, openblas
+, mpiSupport ? false, mpi ? null
 }:
 
 assert mpiSupport -> mpi != null;
 
 stdenv.mkDerivation rec {
   # LAMMPS has weird versioning converted to ISO 8601 format
-  version = "2016-02-16";
+  version = "patch_2Aug2018";
   name = "lammps-${version}";
 
-  src = fetchurl {
-    url = "mirror://sourceforge/lammps/lammps-16Feb16.tar.gz";
-    sha256 = "1yzfbkxma3xa1288rnn66h4w0smbmjkwq1fx1y60pjiw0prmk105";
+  lammps_packages = "asphere body class2 colloid compress coreshell dipole granular kspace manybody mc misc molecule opt peri qeq replica rigid shock snap srd user-reaxc";
+  lammps_includes = "-DLAMMPS_EXCEPTIONS -DLAMMPS_GZIP -DLAMMPS_MEMALIGN=64";
+
+  src = fetchFromGitHub {
+    owner = "lammps";
+    repo = "lammps";
+    rev = "${version}";
+    sha256 = "1ph9pr7s11wgmspmnhxa55bh1pq2cyl8iimfi62lbpbpl9pr1ilc";
   };
 
   passthru = {
     inherit mpi;
   };
 
-  buildInputs = [ fftw libpng ]
+  buildInputs = [ fftw libpng openblas gzip bash ]
   ++ (stdenv.lib.optionals mpiSupport [ mpi ]);
 
   # Must do manual build due to LAMMPS requiring a seperate build for
@@ -27,13 +39,19 @@ stdenv.mkDerivation rec {
   builder = writeText "builder.sh" ''
     source $stdenv/setup
 
-    tar xzf $src
-    cd lammps-*/src
-    make mode=exe ${if mpiSupport then "mpi" else "serial"} SHELL=$SHELL LMP_INC="-DLAMMPS_GZIP -DLAMMPS_PNG" FFT_PATH=-DFFT_FFTW3 FFT_LIB=-lfftw3 JPG_LIB=-lpng
-    make mode=shlib ${if mpiSupport then "mpi" else "serial"} SHELL=$SHELL LMP_INC="-DLAMMPS_GZIP -DLAMMPS_PNG" FFT_PATH=-DFFT_FFTW3 FFT_LIB=-lfftw3 JPG_LIB=-lpng
+    mkdir lammps
+    cp -r $src/lib $src/src lammps
+    chmod -R 755 lammps/src/
+    cd lammps/src
+    for pack in ${lammps_packages}; do make "yes-$pack" SHELL=$SHELL; done
+    make mode=exe ${if mpiSupport then "mpi" else "serial"} SHELL=$SHELL LMP_INC="${lammps_includes}" FFT_PATH=-DFFT_FFTW3 FFT_LIB=-lfftw3 JPG_LIB=-lpng
+    make mode=shlib ${if mpiSupport then "mpi" else "serial"} SHELL=$SHELL LMP_INC="${lammps_includes}" FFT_PATH=-DFFT_FFTW3 FFT_LIB=-lfftw3 JPG_LIB=-lpng
 
     mkdir -p $out/bin
-    cp -v lmp_* $out/bin/lammps
+    cp -v lmp_* $out/bin/
+
+    mkdir -p $out/include
+    cp -v *.h $out/include/
 
     mkdir -p $out/lib
     cp -v liblammps* $out/lib/
@@ -51,5 +69,6 @@ stdenv.mkDerivation rec {
     homepage = http://lammps.sandia.gov;
     license = stdenv.lib.licenses.gpl2;
     platforms = stdenv.lib.platforms.linux;
+    maintainers = with lib.maintainers; [ costrouc ];
   };
 }
diff --git a/pkgs/desktops/gnome-3/core/gnome-desktop/default.nix b/pkgs/desktops/gnome-3/core/gnome-desktop/default.nix
index e909a356866..d6402a3b5b6 100644
--- a/pkgs/desktops/gnome-3/core/gnome-desktop/default.nix
+++ b/pkgs/desktops/gnome-3/core/gnome-desktop/default.nix
@@ -1,4 +1,4 @@
-{ stdenv, fetchurl, pkgconfig, libxslt, which, libX11, gnome3, gtk3, glib
+{ stdenv, fetchurl, substituteAll, pkgconfig, libxslt, which, libX11, gnome3, gtk3, glib
 , intltool, libxml2, xkeyboard_config, isocodes, itstool, wayland
 , libseccomp, bubblewrap, gobjectIntrospection, gtk-doc, docbook_xsl }:
 
@@ -30,18 +30,16 @@ stdenv.mkDerivation rec {
   propagatedBuildInputs = [ gnome3.gsettings-desktop-schemas ];
 
   patches = [
-    ./bubblewrap-paths.patch
+    (substituteAll {
+      src = ./bubblewrap-paths.patch;
+      BUBBLEWRAP_BIN = "${bubblewrap}/bin/bwrap";
+    })
   ];
 
   configureFlags = [
     "--enable-gtk-doc"
   ];
 
-  postPatch = ''
-    substituteInPlace libgnome-desktop/gnome-desktop-thumbnail-script.c --subst-var-by \
-      BUBBLEWRAP_BIN "${bubblewrap}/bin/bwrap"
-  '';
-
   passthru = {
     updateScript = gnome3.updateScript {
       packageName = "gnome-desktop";
diff --git a/pkgs/desktops/gnome-3/core/gnome-keyring/default.nix b/pkgs/desktops/gnome-3/core/gnome-keyring/default.nix
index acb32bc174c..cce192c9f29 100644
--- a/pkgs/desktops/gnome-3/core/gnome-keyring/default.nix
+++ b/pkgs/desktops/gnome-3/core/gnome-keyring/default.nix
@@ -1,6 +1,6 @@
-{ stdenv, fetchurl, pkgconfig, dbus, libgcrypt, libtasn1, pam, python2, glib, libxslt
-, intltool, pango, gcr, gdk_pixbuf, atk, p11-kit, openssh, wrapGAppsHook
-, docbook_xsl, docbook_xml_dtd_42, gnome3 }:
+{ stdenv, fetchurl, pkgconfig, dbus, libgcrypt, pam, python2, glib, libxslt
+, gettext, gcr, libcap_ng, libselinux, p11-kit, openssh, wrapGAppsHook
+, docbook_xsl, docbook_xml_dtd_43, gnome3 }:
 
 stdenv.mkDerivation rec {
   name = "gnome-keyring-${version}";
@@ -11,21 +11,15 @@ stdenv.mkDerivation rec {
     sha256 = "0sk4las4ji8wv9nx8mldzqccmpmkvvr9pdwv9imj26r10xyin5w1";
   };
 
-  passthru = {
-    updateScript = gnome3.updateScript { packageName = "gnome-keyring"; attrPath = "gnome3.gnome-keyring"; };
-  };
-
   outputs = [ "out" "dev" ];
 
-  buildInputs = with gnome3; [
-    dbus libgcrypt pam gtk3 libgnome-keyring openssh
-    pango gcr gdk_pixbuf atk p11-kit
+  buildInputs = [
+    glib libgcrypt pam openssh libcap_ng libselinux
+    gcr p11-kit
   ];
 
-  propagatedBuildInputs = [ glib libtasn1 libxslt ];
-
   nativeBuildInputs = [
-    pkgconfig intltool docbook_xsl docbook_xml_dtd_42 wrapGAppsHook
+    pkgconfig gettext libxslt docbook_xsl docbook_xml_dtd_43 wrapGAppsHook
   ];
 
   configureFlags = [
@@ -48,6 +42,13 @@ stdenv.mkDerivation rec {
       make check
   '';
 
+  passthru = {
+    updateScript = gnome3.updateScript {
+      packageName = "gnome-keyring";
+      attrPath = "gnome3.gnome-keyring";
+    };
+  };
+
   meta = with stdenv.lib; {
     description = "Collection of components in GNOME that store secrets, passwords, keys, certificates and make them available to applications";
     homepage = https://wiki.gnome.org/Projects/GnomeKeyring;
diff --git a/pkgs/desktops/gnome-3/core/gnome-shell/default.nix b/pkgs/desktops/gnome-3/core/gnome-shell/default.nix
index b4d309e1981..8e09c960e75 100644
--- a/pkgs/desktops/gnome-3/core/gnome-shell/default.nix
+++ b/pkgs/desktops/gnome-3/core/gnome-shell/default.nix
@@ -2,7 +2,7 @@
 , python3Packages, libsoup, polkit, clutter, networkmanager, docbook_xsl , docbook_xsl_ns, at-spi2-core
 , libstartup_notification, telepathy-glib, telepathy-logger, libXtst, unzip, glibcLocales, shared-mime-info
 , libgweather, libcanberra-gtk3, librsvg, geoclue2, perl, docbook_xml_dtd_42, desktop-file-utils
-, libpulseaudio, libical, gobjectIntrospection, gstreamer, wrapGAppsHook
+, libpulseaudio, libical, gobjectIntrospection, gstreamer, wrapGAppsHook, libxslt
 , accountsservice, gdk_pixbuf, gdm, upower, ibus, networkmanagerapplet
 , sassc, systemd, gst_all_1 }:
 
@@ -27,7 +27,7 @@ in stdenv.mkDerivation rec {
 
   nativeBuildInputs = [
     meson ninja pkgconfig gettext docbook_xsl docbook_xsl_ns docbook_xml_dtd_42 perl wrapGAppsHook glibcLocales
-    sassc desktop-file-utils
+    sassc desktop-file-utils libxslt.bin
   ];
   buildInputs = with gnome3; [
     systemd caribou
diff --git a/pkgs/desktops/xfce4-13/xfce4-settings/default.nix b/pkgs/desktops/xfce4-13/xfce4-settings/default.nix
index d08c1f96fdd..6eb917fd76f 100644
--- a/pkgs/desktops/xfce4-13/xfce4-settings/default.nix
+++ b/pkgs/desktops/xfce4-13/xfce4-settings/default.nix
@@ -1,4 +1,4 @@
-{ mkXfceDerivation, automakeAddFlags, dbus-glib, exo, garcon, gtk3
+{ mkXfceDerivation, automakeAddFlags, exo, garcon, gtk3
 , libnotify ? null, libxfce4ui, libxfce4util, libxklavier ? null
 , upower ? null, xfconf, xf86inputlibinput ? null }:
 
@@ -19,7 +19,6 @@ mkXfceDerivation rec {
   nativeBuildInputs = [ automakeAddFlags ];
 
   buildInputs = [
-    dbus-glib
     exo
     garcon
     gtk3
diff --git a/pkgs/development/libraries/mesa/default.nix b/pkgs/development/libraries/mesa/default.nix
index 063ed381e01..0a8a3c75a1c 100644
--- a/pkgs/development/libraries/mesa/default.nix
+++ b/pkgs/development/libraries/mesa/default.nix
@@ -63,7 +63,7 @@ let
 in
 
 let
-  version = "18.1.5";
+  version = "18.1.7";
   branch  = head (splitString "." version);
 in
 
@@ -77,7 +77,7 @@ let self = stdenv.mkDerivation {
       "ftp://ftp.freedesktop.org/pub/mesa/older-versions/${branch}.x/${version}/mesa-${version}.tar.xz"
       "https://mesa.freedesktop.org/archive/mesa-${version}.tar.xz"
     ];
-    sha256 = "69dbe6f1a6660386f5beb85d4fcf003ee23023ed7b9a603de84e9a37e8d98dea";
+    sha256 = "655e3b32ce3bdddd5e6e8768596e5d4bdef82d0dd37067c324cc4b2daa207306";
   };
 
   prePatch = "patchShebangs .";
@@ -100,6 +100,7 @@ let self = stdenv.mkDerivation {
     "--with-dri-driverdir=$(drivers)/lib/dri"
     "--with-dri-searchpath=${libglvnd.driverLink}/lib/dri"
     "--with-platforms=x11,wayland,drm"
+    "--enable-texture-float"
   ]
   ++ (optional (galliumDrivers != [])
       ("--with-gallium-drivers=" +
diff --git a/pkgs/development/libraries/pagmo2/default.nix b/pkgs/development/libraries/pagmo2/default.nix
new file mode 100644
index 00000000000..367cef46dc4
--- /dev/null
+++ b/pkgs/development/libraries/pagmo2/default.nix
@@ -0,0 +1,46 @@
+{ lib
+, fetchFromGitHub
+, stdenv
+, cmake
+, eigen
+, nlopt
+, ipopt
+, boost
+, writeText
+}:
+
+stdenv.mkDerivation rec {
+  name = "pagmo2-${version}";
+  version = "2.8";
+
+  src = fetchFromGitHub {
+     owner = "esa";
+     repo = "pagmo2";
+     rev = "v${version}";
+     sha256 = "1xwxamcn3fkwr62jn6bkanrwy0cvsksf75hfwx4fvl56awnbz41z";
+  };
+
+  buildInputs = [ cmake eigen nlopt ipopt boost ];
+
+  preBuild = ''
+    cp -r $src/* .
+  '';
+
+  cmakeFlags = [ "-DPAGMO_BUILD_TESTS=no"
+                 "-DPAGMO_WITH_EIGEN3=yes" "-DPAGMO_WITH_NLOPT=yes"
+                 "-DNLOPT_LIBRARY=${nlopt}/lib/libnlopt_cxx.so" "-DPAGMO_WITH_IPOPT=yes"
+                 "-DCMAKE_CXX_FLAGS='-fuse-ld=gold'" ];
+
+  checkPhase = ''
+    ctest
+  '';
+
+  # All but one test pass skip for now (tests also take about 30 min to compile)
+  doCheck = false;
+
+  meta = {
+    homepage = https://esa.github.io/pagmo2/;
+    description = "Scientific library for massively parallel optimization";
+    license = stdenv.lib.licenses.gpl3Plus;
+  };
+}
diff --git a/pkgs/development/libraries/science/math/openblas/default.nix b/pkgs/development/libraries/science/math/openblas/default.nix
index b5efdc58584..3f271d01502 100644
--- a/pkgs/development/libraries/science/math/openblas/default.nix
+++ b/pkgs/development/libraries/science/math/openblas/default.nix
@@ -136,6 +136,20 @@ stdenv.mkDerivation rec {
   doCheck = true;
   checkTarget = "tests";
 
+  postInstall = ''
+    # Write pkgconfig aliases. Upstream report:
+    # https://github.com/xianyi/OpenBLAS/issues/1740
+    for alias in blas cblas lapack; do
+      cat <<EOF > $out/lib/pkgconfig/openblas-$alias.pc
+Name: $alias
+Version: ${version}
+Description: $alias provided by the OpenBLAS package.
+Cflags: -I$out/include
+Libs: -L$out/lib -lopenblas
+EOF
+    done
+  '';
+
   meta = with stdenv.lib; {
     description = "Basic Linear Algebra Subprograms";
     license = licenses.bsd3;
diff --git a/pkgs/development/libraries/umockdev/default.nix b/pkgs/development/libraries/umockdev/default.nix
index 9ee2dadb8b0..912bcac55cd 100644
--- a/pkgs/development/libraries/umockdev/default.nix
+++ b/pkgs/development/libraries/umockdev/default.nix
@@ -1,10 +1,12 @@
-{ stdenv, fetchFromGitHub, autoreconfHook, libtool
+{ stdenv, fetchFromGitHub, autoreconfHook, umockdev, gobjectIntrospection
 , pkgconfig, glib, systemd, libgudev, vala }:
 
 stdenv.mkDerivation rec {
   name = "umockdev-${version}";
   version = "0.12";
 
+  outputs = [ "bin" "out" "dev" "doc" ];
+
   src = fetchFromGitHub {
     owner  = "martinpitt";
     repo   = "umockdev";
@@ -19,7 +21,7 @@ stdenv.mkDerivation rec {
 
   buildInputs = [ glib systemd libgudev ];
 
-  nativeBuildInputs = [ autoreconfHook libtool pkgconfig vala ];
+  nativeBuildInputs = [ autoreconfHook pkgconfig vala gobjectIntrospection ];
 
   enableParallelBuilding = true;
 
diff --git a/pkgs/development/perl-modules/DB_File/default.nix b/pkgs/development/perl-modules/DB_File/default.nix
index b34ea387366..b3ca12421e4 100644
--- a/pkgs/development/perl-modules/DB_File/default.nix
+++ b/pkgs/development/perl-modules/DB_File/default.nix
@@ -1,11 +1,11 @@
 {fetchurl, buildPerlPackage, db}:
 
 buildPerlPackage rec {
-  name = "DB_File-1.841";
+  name = "DB_File-1.842";
 
   src = fetchurl {
     url = "mirror://cpan/authors/id/P/PM/PMQS/${name}.tar.gz";
-    sha256 = "11fks42kgscpia0mxx4lc9krm7q4gv6w7m5h3m2jr3dl7viv36hn";
+    sha256 = "0w2d99vs9qarng2f9fpg3gchfdzy6an13507jhclcl8wv183h5hg";
   };
 
   preConfigure = ''
diff --git a/pkgs/development/python-modules/APScheduler/default.nix b/pkgs/development/python-modules/APScheduler/default.nix
index 5e108cd7dcf..f3c8c57f576 100644
--- a/pkgs/development/python-modules/APScheduler/default.nix
+++ b/pkgs/development/python-modules/APScheduler/default.nix
@@ -20,11 +20,11 @@
 
 buildPythonPackage rec {
   pname = "APScheduler";
-  version = "3.5.1";
+  version = "3.5.3";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "952c8f46a11f32b9d5bfbe3e347dac2cdf0680d8b4799590dc9c3a9865b73b65";
+    sha256 = "6599bc78901ee7e9be85cbd073d9cc155c42d2bc867c5cde4d4d1cc339ebfbeb";
   };
 
   buildInputs = [
diff --git a/pkgs/development/python-modules/Flask-PyMongo/default.nix b/pkgs/development/python-modules/Flask-PyMongo/default.nix
index 6a14607ad27..862fd84c492 100644
--- a/pkgs/development/python-modules/Flask-PyMongo/default.nix
+++ b/pkgs/development/python-modules/Flask-PyMongo/default.nix
@@ -8,11 +8,11 @@
 
 buildPythonPackage rec {
   pname = "Flask-PyMongo";
-  version = "2.0.1";
+  version = "2.1.0";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "6a02add52ac245064720c2bb8b02074b9a5a0d9498279510ea2a537512fd3fa5";
+    sha256 = "0b99dd99985660ebbc4b34bb44550f88a527cbc573faa01febccce3c4ab28347";
   };
 
   checkInputs = [ pytest ];
diff --git a/pkgs/development/python-modules/XlsxWriter/default.nix b/pkgs/development/python-modules/XlsxWriter/default.nix
index be5ad2a5c1c..71229b886e7 100644
--- a/pkgs/development/python-modules/XlsxWriter/default.nix
+++ b/pkgs/development/python-modules/XlsxWriter/default.nix
@@ -2,11 +2,11 @@
 
 buildPythonPackage rec {
   pname = "XlsxWriter";
-  version = "1.0.5";
+  version = "1.0.9";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "bd4661c04a68621cb2ebc07c38b8b2e98e30bf213a16e1cf3675b61e26ca9bf2";
+    sha256 = "98a94b32d4929d3e34595b4654b8e7f951182f540056b9cb734c88899912f729";
   };
 
   meta = {
diff --git a/pkgs/development/python-modules/absl-py/default.nix b/pkgs/development/python-modules/absl-py/default.nix
index 1cb5275a6c3..a087eaeca83 100644
--- a/pkgs/development/python-modules/absl-py/default.nix
+++ b/pkgs/development/python-modules/absl-py/default.nix
@@ -6,11 +6,11 @@
 
 buildPythonPackage rec {
   pname = "absl-py";
-  version = "0.2.2";
+  version = "0.4.1";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "e0eb8358b549552b1cc5972350bc3e41dd0a926c15b3ff95ce60f3c78c80824c";
+    sha256 = "1e6e70506fb4d867cf269af7bcc27b744c36bbc4c516f0f8ccf2039956deea72";
   };
 
   propagatedBuildInputs = [ six ];
diff --git a/pkgs/development/python-modules/aiofiles/default.nix b/pkgs/development/python-modules/aiofiles/default.nix
index 572c18171d1..55d68f93f2c 100644
--- a/pkgs/development/python-modules/aiofiles/default.nix
+++ b/pkgs/development/python-modules/aiofiles/default.nix
@@ -9,11 +9,11 @@
 
 buildPythonPackage rec {
   pname = "aiofiles";
-  version = "0.3.2";
+  version = "0.4.0";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "852a493a877b73e11823bfd4e8e5ef2610d70d12c9eaed961bcd9124d8de8c10";
+    sha256 = "021ea0ba314a86027c166ecc4b4c07f2d40fc0f4b3a950d1868a0f2571c2bbee";
   };
 
   disabled = pythonOlder "3.3";
diff --git a/pkgs/development/python-modules/aiohue/default.nix b/pkgs/development/python-modules/aiohue/default.nix
index 1492a15aadf..d5572bb6d1d 100644
--- a/pkgs/development/python-modules/aiohue/default.nix
+++ b/pkgs/development/python-modules/aiohue/default.nix
@@ -2,11 +2,11 @@
 
 buildPythonPackage rec {
   pname = "aiohue";
-  version = "1.6.0";
+  version = "1.7.0";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "87f0f86865e88ea715ab358b1e5f2838b79ee7cdc0bdf762e9ed60aaf4c8bd4a";
+    sha256 = "26989babdc3f38575164b60b9536309271d58db005a03045b6e9cca4fc5201d8";
   };
 
   propagatedBuildInputs = [ aiohttp ];
diff --git a/pkgs/development/python-modules/allpairspy/default.nix b/pkgs/development/python-modules/allpairspy/default.nix
index e21b43c60e0..d1f97d8e7c7 100644
--- a/pkgs/development/python-modules/allpairspy/default.nix
+++ b/pkgs/development/python-modules/allpairspy/default.nix
@@ -2,11 +2,11 @@
 
 buildPythonPackage rec {
   pname = "allpairspy";
-  version = "2.4.0";
+  version = "2.4.1";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "9fb7962ee523bd96c5098cd3c97ac1b8eb73021d3df9314657ee9de00f52e034";
+    sha256 = "e8b35751f91692bf0318091b3f44cdf9bbbe3f37a2ff4786eaffc09dc7114fb3";
   };
 
   propagatedBuildInputs = [ six ];
diff --git a/pkgs/development/python-modules/argon2_cffi/default.nix b/pkgs/development/python-modules/argon2_cffi/default.nix
index ce371076256..120928656b4 100644
--- a/pkgs/development/python-modules/argon2_cffi/default.nix
+++ b/pkgs/development/python-modules/argon2_cffi/default.nix
@@ -9,12 +9,12 @@
 
 buildPythonPackage rec {
   pname = "argon2_cffi";
-  version = "18.1.0";
+  version = "18.3.0";
   name    = "${pname}-${version}";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "7e4b75611b73f53012117ad21cdde7a17b32d1e99ff6799f22d827eb83a2a59b";
+    sha256 = "003f588de43a817af6ecc1c06103fa0801de63849db3cb0f37576bb2da29043d";
   };
 
   propagatedBuildInputs = [ cffi six ];
diff --git a/pkgs/development/python-modules/ase/default.nix b/pkgs/development/python-modules/ase/default.nix
new file mode 100644
index 00000000000..1f7b9419278
--- /dev/null
+++ b/pkgs/development/python-modules/ase/default.nix
@@ -0,0 +1,36 @@
+{ lib
+, fetchurl
+, buildPythonPackage
+, numpy
+, scipy
+, matplotlib
+, flask
+, pillow
+, psycopg2
+}:
+
+buildPythonPackage rec {
+  version = "3.16.2";
+  pname = "ase";
+
+  src = fetchurl {
+     url = "https://gitlab.com/${pname}/${pname}/-/archive/${version}/${pname}-${version}.tar.gz";
+     sha256 = "171j3f4a261cfnqjq98px5fldxql65i3jgf60wc945xvh0mbc8ds";
+  };
+
+  propagatedBuildInputs = [ numpy scipy matplotlib flask pillow psycopg2 ];
+
+  checkPhase = ''
+    $out/bin/ase test
+  '';
+
+  # tests just hang most likely due to something with subprocesses and cli
+  doCheck = false;
+
+  meta = {
+    description = "Atomic Simulation Environment";
+    homepage = https://wiki.fysik.dtu.dk/ase/;
+    license = lib.licenses.lgpl21Plus;
+    maintainers = with lib.maintainers; [ costrouc ];
+  };
+}
diff --git a/pkgs/development/python-modules/astroid/default.nix b/pkgs/development/python-modules/astroid/default.nix
index ea087ce4f5f..ccf6f405526 100644
--- a/pkgs/development/python-modules/astroid/default.nix
+++ b/pkgs/development/python-modules/astroid/default.nix
@@ -5,13 +5,13 @@
 
 buildPythonPackage rec {
   pname = "astroid";
-  version = "2.0.1";
+  version = "2.0.4";
 
   disabled = pythonOlder "3.4";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "218e36cf8d98a42f16214e8670819ce307fa707d1dcf7f9af84c7aede1febc7f";
+    sha256 = "c7013d119ec95eb626f7a2011f0b63d0c9a095df9ad06d8507b37084eada1a8d";
   };
 
   # From astroid/__pkginfo__.py
diff --git a/pkgs/development/python-modules/astropy/default.nix b/pkgs/development/python-modules/astropy/default.nix
index 4901b798955..acbd7c2ec65 100644
--- a/pkgs/development/python-modules/astropy/default.nix
+++ b/pkgs/development/python-modules/astropy/default.nix
@@ -7,7 +7,7 @@
 
 buildPythonPackage rec {
   pname = "astropy";
-  version = "3.0.3";
+  version = "3.0.4";
 
   disabled = !isPy3k; # according to setup.py
 
@@ -15,7 +15,7 @@ buildPythonPackage rec {
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "6af07abe5e263820a3dec93832a6ad74005013071490e125afbc6514411721da";
+    sha256 = "f5d37d20632ba74bd0b12a85179c12f64a9ea037ffc916d8a2de3be4f4656c76";
   };
 
   propagatedBuildInputs = [ pytest numpy ]; # yes it really has pytest in install_requires
diff --git a/pkgs/development/python-modules/async_generator/default.nix b/pkgs/development/python-modules/async_generator/default.nix
index 4f46376b62d..6bf77ecd75e 100644
--- a/pkgs/development/python-modules/async_generator/default.nix
+++ b/pkgs/development/python-modules/async_generator/default.nix
@@ -2,13 +2,13 @@
 
 buildPythonPackage rec {
   pname = "async_generator";
-  version = "1.9";
+  version = "1.10";
 
   disabled = pythonOlder "3.5";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "b7d5465c6174fe86dba498ececb175f93a6097ffb7cc91946405e1f05b848371";
+    sha256 = "6ebb3d106c12920aaae42ccb6f787ef5eefdcdd166ea3d628fa8476abe712144";
   };
 
   checkInputs = [ pytest pytest-asyncio ];
diff --git a/pkgs/development/python-modules/autobahn/default.nix b/pkgs/development/python-modules/autobahn/default.nix
index 30479ce8266..87a337a154d 100644
--- a/pkgs/development/python-modules/autobahn/default.nix
+++ b/pkgs/development/python-modules/autobahn/default.nix
@@ -1,22 +1,22 @@
 { stdenv, buildPythonPackage, fetchPypi, isPy3k, isPy33,
   unittest2, mock, pytest, trollius, asyncio,
-  pytest-asyncio, futures,
+  pytest-asyncio, futures, cffi,
   six, twisted, txaio, zope_interface
 }:
 buildPythonPackage rec {
   pname = "autobahn";
-  version = "18.6.1";
+  version = "18.8.1";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "2f41bfc512ec482044fa8cfa74182118dedd87e03b3494472d9ff1b5a1e27d24";
+    sha256 = "b69858e0be4bff8437b0bd82a0db1cbef7405e16bd9354ba587c043d6d5e1ad9";
   };
 
   # Upstream claim python2 support, but tests require pytest-asyncio which
   # is pythn3 only. Therefore, tests are skipped for python2.
   doCheck = isPy3k;
-  buildInputs = stdenv.lib.optionals isPy3k [ unittest2 mock pytest pytest-asyncio ];
-  propagatedBuildInputs = [ six twisted zope_interface txaio ] ++
+  checkInputs = stdenv.lib.optionals isPy3k [ unittest2 mock pytest pytest-asyncio ];
+  propagatedBuildInputs = [ cffi six twisted zope_interface txaio ] ++
     (stdenv.lib.optional isPy33 asyncio) ++
     (stdenv.lib.optionals (!isPy3k) [ trollius futures ]);
 
@@ -29,6 +29,5 @@ buildPythonPackage rec {
     homepage    = "https://crossbar.io/autobahn";
     license     = licenses.mit;
     maintainers = with maintainers; [ nand0p ];
-    platforms   = platforms.all;
   };
 }
diff --git a/pkgs/development/python-modules/aws-adfs/default.nix b/pkgs/development/python-modules/aws-adfs/default.nix
index c42ad6f1d6c..bce64a635e3 100644
--- a/pkgs/development/python-modules/aws-adfs/default.nix
+++ b/pkgs/development/python-modules/aws-adfs/default.nix
@@ -2,12 +2,12 @@
 , pytest, pytestrunner, pytestcov, mock, glibcLocales, lxml, boto3, requests, click, configparser }:
 
 buildPythonPackage rec {
-  version = "0.12.0";
+  version = "0.12.1";
   pname = "aws-adfs";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "1cjrm61k6905dmhgrqyc5caxx5hbhj3sr6cx4r6sbdyz453i7pc6";
+    sha256 = "72725d7005252b96ccfa9719fe4beec2b86301bff894d4d97a50fc1d05393fd8";
   };
 
   # Relax version constraint
diff --git a/pkgs/development/python-modules/backports_lzma/default.nix b/pkgs/development/python-modules/backports_lzma/default.nix
index 64fcc2c0d5d..82025df8b9e 100644
--- a/pkgs/development/python-modules/backports_lzma/default.nix
+++ b/pkgs/development/python-modules/backports_lzma/default.nix
@@ -24,6 +24,9 @@ if !(pythonOlder "3.3") then null else buildPythonPackage rec {
     ${python.interpreter} test/test_lzma.py
   '';
 
+  # Relative import does not seem to function.
+  doCheck = false;
+
   meta = {
     description = "Backport of Python 3.3's 'lzma' module for XZ/LZMA compressed files";
     homepage = https://github.com/peterjc/backports.lzma;
diff --git a/pkgs/development/python-modules/beautifulsoup4/default.nix b/pkgs/development/python-modules/beautifulsoup4/default.nix
index 6ae838265b1..7cf4f36a2f0 100644
--- a/pkgs/development/python-modules/beautifulsoup4/default.nix
+++ b/pkgs/development/python-modules/beautifulsoup4/default.nix
@@ -2,11 +2,11 @@
 
 buildPythonPackage rec {
   pname = "beautifulsoup4";
-  version = "4.6.0";
+  version = "4.6.3";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "12cf0ygpz9srpfh9gx2f9ba0swa1rzypv3sm4r0hmjyw6b4nm2w0";
+    sha256 = "90f8e61121d6ae58362ce3bed8cd997efb00c914eae0ff3d363c32f9a9822d10";
   };
 
   buildInputs = [ nose ];
diff --git a/pkgs/development/python-modules/bitmath/default.nix b/pkgs/development/python-modules/bitmath/default.nix
index bb2e6046886..092ad6c1003 100644
--- a/pkgs/development/python-modules/bitmath/default.nix
+++ b/pkgs/development/python-modules/bitmath/default.nix
@@ -2,11 +2,11 @@
 
 buildPythonPackage rec {
   pname = "bitmath";
-  version = "1.3.1.2";
+  version = "1.3.3.1";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "1k8d1wmxqjc8cqzaixpxf45k6dl1kqhblr0g4wyjl0qa18q8wasd";
+    sha256 = "293325f01e65defe966853111df11d39215eb705a967cb115851da8c4cfa3eb8";
   };
 
   checkInputs = [ (if isPy3k then progressbar33 else progressbar231) mock ];
diff --git a/pkgs/development/python-modules/bleach/default.nix b/pkgs/development/python-modules/bleach/default.nix
index 786564b92e0..3c5f1d44190 100644
--- a/pkgs/development/python-modules/bleach/default.nix
+++ b/pkgs/development/python-modules/bleach/default.nix
@@ -9,11 +9,11 @@
 
 buildPythonPackage rec {
   pname = "bleach";
-  version = "2.1.3";
+  version = "2.1.4";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "eb7386f632349d10d9ce9d4a838b134d4731571851149f9cc2c05a9a837a9a44";
+    sha256 = "0ee95f6167129859c5dce9b1ca291ebdb5d8cd7e382ca0e237dfd0dad63f63d8";
   };
 
   checkInputs = [ pytest pytestrunner ];
diff --git a/pkgs/development/python-modules/bootstrapped-pip/default.nix b/pkgs/development/python-modules/bootstrapped-pip/default.nix
index b320db51e3c..613be1f7d6b 100644
--- a/pkgs/development/python-modules/bootstrapped-pip/default.nix
+++ b/pkgs/development/python-modules/bootstrapped-pip/default.nix
@@ -9,9 +9,9 @@ let
   };
   setuptools_source = fetchPypi {
     pname = "setuptools";
-    version = "40.0.0";
+    version = "40.2.0";
     format = "wheel";
-    sha256 = "d68abee4eed409fbe8c302ac4d8429a1ffef912cd047a903b5701c024048dd49";
+    sha256 = "ea3796a48a207b46ea36a9d26de4d0cc87c953a683a7b314ea65d666930ea8e6";
   };
 
 in stdenv.mkDerivation rec {
diff --git a/pkgs/development/python-modules/boto3/default.nix b/pkgs/development/python-modules/boto3/default.nix
index dca7844dec9..31f050007a6 100644
--- a/pkgs/development/python-modules/boto3/default.nix
+++ b/pkgs/development/python-modules/boto3/default.nix
@@ -13,13 +13,13 @@
 
 buildPythonPackage rec {
   pname =  "boto3";
-  version = "1.7.57";
+  version = "1.7.84";
 
   src = fetchFromGitHub {
     owner = "boto";
     repo  = "boto3";
     rev   = version;
-    sha256 = "0rp3vclx7mvfl6isa47m7dzlrf33qb9vj53p0gj4cw3mgl14cnbl";
+    sha256 = "0d9kqjqmnn53p1xpmdbbjxcxv2482yx3vjhxw8izp0mpq58i5c14";
   };
 
   propagatedBuildInputs = [ botocore jmespath s3transfer ] ++ lib.optionals (!isPy3k) [ futures ];
diff --git a/pkgs/development/python-modules/botocore/default.nix b/pkgs/development/python-modules/botocore/default.nix
index f1475aed693..989b6e944de 100644
--- a/pkgs/development/python-modules/botocore/default.nix
+++ b/pkgs/development/python-modules/botocore/default.nix
@@ -11,11 +11,11 @@
 
 buildPythonPackage rec {
   pname = "botocore";
-  version = "1.10.65";
+  version = "1.10.84";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "35f626029a6b17bfd503ce3379b121606e3f965edcab2612bc75ce8603fdf08c";
+    sha256 = "d3e4b5a2c903ea30d19d41ea2f65d0e51dce54f4f4c4dfd6ecd7b04f240844a8";
   };
 
   propagatedBuildInputs = [
diff --git a/pkgs/development/python-modules/bottleneck/default.nix b/pkgs/development/python-modules/bottleneck/default.nix
index c9ca8f7ec04..c4db013ea34 100644
--- a/pkgs/development/python-modules/bottleneck/default.nix
+++ b/pkgs/development/python-modules/bottleneck/default.nix
@@ -1,6 +1,7 @@
 { buildPythonPackage
 , fetchPypi
 , nose
+, pytest
 , numpy
 , python
 }:
@@ -15,10 +16,10 @@ buildPythonPackage rec {
     sha256 = "6efcde5f830aed64feafca0359b51db0e184c72af8ba6675b4a99f263922eb36";
   };
 
-  checkInputs = [ nose ];
+  checkInputs = [ pytest nose ];
   propagatedBuildInputs = [ numpy ];
   checkPhase = ''
-    nosetests -v $out/${python.sitePackages}
+    py.test -p no:warnings $out/${python.sitePackages}
   '';
   postPatch = ''
     substituteInPlace setup.py --replace "__builtins__.__NUMPY_SETUP__ = False" ""
diff --git a/pkgs/development/python-modules/breathe/default.nix b/pkgs/development/python-modules/breathe/default.nix
index a76b7b2611b..645f75eb323 100644
--- a/pkgs/development/python-modules/breathe/default.nix
+++ b/pkgs/development/python-modules/breathe/default.nix
@@ -1,12 +1,12 @@
 { lib, fetchPypi, buildPythonPackage, docutils, six, sphinx, isPy3k }:
 
 buildPythonPackage rec {
-  version = "4.9.1";
+  version = "4.10.0";
   pname = "breathe";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "76e1f3706efeda2610d9a8e7b421d2877ff0654a3fe6d3190a8686536111a684";
+    sha256 = "e94370b8b607a32d9611ed8246e635f02c21dc6847f04e888a00f66a12694eff";
   };
 
   propagatedBuildInputs = [ docutils six sphinx ];
diff --git a/pkgs/development/python-modules/btrees/default.nix b/pkgs/development/python-modules/btrees/default.nix
index c031c872da3..c96d305a7f6 100644
--- a/pkgs/development/python-modules/btrees/default.nix
+++ b/pkgs/development/python-modules/btrees/default.nix
@@ -9,7 +9,7 @@
 
 buildPythonPackage rec {
   pname = "BTrees";
-  version = "4.5.0";
+  version = "4.5.1";
 
   buildInputs = [ transaction ];
   propagatedBuildInputs = [ persistent zope_interface ];
@@ -17,7 +17,7 @@ buildPythonPackage rec {
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "46b02cb69b26a5238db771ea1955b503df73ecf254bb8063af4c61999fc75b5c";
+    sha256 = "dcc096c3cf92efd6b9365951f89118fd30bc209c9af83bf050a28151a9992786";
   };
 
   meta = with stdenv.lib; {
diff --git a/pkgs/development/python-modules/bugwarrior/default.nix b/pkgs/development/python-modules/bugwarrior/default.nix
index ada8397f975..844aebbbb96 100644
--- a/pkgs/development/python-modules/bugwarrior/default.nix
+++ b/pkgs/development/python-modules/bugwarrior/default.nix
@@ -5,11 +5,11 @@
 
 buildPythonPackage rec {
   pname = "bugwarrior";
-  version = "1.5.1";
+  version = "1.6.0";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "0kxknjbw5kchd88i577vlzibg8j60r7zzdhbnragj9wg5s3w60xb";
+    sha256 = "cfa4fac19b4f4638928347b8fe192315f72813c3e8ed668867e5891338c7e4ec";
   };
 
   buildInputs = [ mock unittest2 nose /* jira megaplan */ ];
diff --git a/pkgs/development/python-modules/buildout/default.nix b/pkgs/development/python-modules/buildout/default.nix
index 9efc53ebe6d..c75b9fdb6cc 100644
--- a/pkgs/development/python-modules/buildout/default.nix
+++ b/pkgs/development/python-modules/buildout/default.nix
@@ -2,11 +2,11 @@
 
 buildPythonPackage rec {
   pname = "zc.buildout";
-  version = "2.2.5";
+  version = "2.12.1";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "fb08f24f9e51e647e29d714f6e9ad51a4ea28673dddeed831315617bb5a805d0";
+    sha256 = "1e180b62fd129a68cb3a9ec8eb0ef457e18921269a93e87ef2cc34519415332d";
   };
 
   meta = with stdenv.lib; {
diff --git a/pkgs/development/python-modules/cairocffi/cairocffi-0.8.1-cairo-1.15.12.patch b/pkgs/development/python-modules/cairocffi/cairocffi-0.8.1-cairo-1.15.12.patch
deleted file mode 100644
index 4d142275b9e..00000000000
--- a/pkgs/development/python-modules/cairocffi/cairocffi-0.8.1-cairo-1.15.12.patch
+++ /dev/null
@@ -1,24 +0,0 @@
-diff --git a/cairocffi/test_cairo.py b/cairocffi/test_cairo.py
-index 1588349..5452910 100644
---- a/cairocffi/test_cairo.py
-+++ b/cairocffi/test_cairo.py
-@@ -292,7 +292,8 @@ def test_pdf_surface():
-         pdf_bytes = file_obj.getvalue()
-         assert pdf_bytes.startswith(b'%PDF')
-         assert b'/MediaBox [ 0 0 123 432 ]' in pdf_bytes
--        assert pdf_bytes.count(b'/Type /Page\n') == 1
-+        assert pdf_bytes.count(b'/Type /Pages') == 1
-+        assert pdf_bytes.count(b'/Type /Page') == 2
- 
-     file_obj = io.BytesIO()
-     surface = PDFSurface(file_obj, 1, 1)
-@@ -306,7 +307,8 @@ def test_pdf_surface():
-     assert b'/MediaBox [ 0 0 1 1 ]' not in pdf_bytes
-     assert b'/MediaBox [ 0 0 12 100 ]' in pdf_bytes
-     assert b'/MediaBox [ 0 0 42 700 ]' in pdf_bytes
--    assert pdf_bytes.count(b'/Type /Page\n') == 2
-+    assert pdf_bytes.count(b'/Type /Pages') == 1
-+    assert pdf_bytes.count(b'/Type /Page') == 3
- 
- 
- def test_svg_surface():
diff --git a/pkgs/development/python-modules/cairocffi/default.nix b/pkgs/development/python-modules/cairocffi/default.nix
index 13d00d0529c..bdd11fb3de6 100644
--- a/pkgs/development/python-modules/cairocffi/default.nix
+++ b/pkgs/development/python-modules/cairocffi/default.nix
@@ -17,11 +17,11 @@
 
 buildPythonPackage rec {
   pname = "cairocffi";
-  version = "0.8.1";
+  version = "0.9.0";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "0y373vafv7q35msg7gqdn7niifr3j4j4n070hflxshahs59irss7";
+    sha256 = "15386c3a9e08823d6826c4491eaccc7b7254b1dc587a3b9ce60c350c3f990337";
   };
 
   LC_ALL = "en_US.UTF-8";
@@ -49,7 +49,6 @@ buildPythonPackage rec {
       gdk_pixbuf = gdk_pixbuf.out;
     })
     ./fix_test_scaled_font.patch
-    ./cairocffi-0.8.1-cairo-1.15.12.patch
   ];
 
   meta = with lib; {
diff --git a/pkgs/development/python-modules/celery/default.nix b/pkgs/development/python-modules/celery/default.nix
index 71911da08f4..df260b3adb7 100644
--- a/pkgs/development/python-modules/celery/default.nix
+++ b/pkgs/development/python-modules/celery/default.nix
@@ -2,7 +2,18 @@
   pytest, case, kombu, billiard, pytz, anyjson, amqp, eventlet
 }:
 
-buildPythonPackage rec {
+let
+
+  # Needed for celery
+  pytest_32 = pytest.overridePythonAttrs( oldAttrs: rec {
+    version = "3.2.5";
+    src = oldAttrs.src.override {
+      inherit version;
+      sha256 = "6d5bd4f7113b444c55a3bbb5c738a3dd80d43563d063fc42dcb0aaefbdd78b81";
+    };
+  });
+
+in buildPythonPackage rec {
   pname = "celery";
   version = "4.2.0";
 
@@ -27,7 +38,7 @@ buildPythonPackage rec {
     unset NIX_REDIRECTS LD_PRELOAD
   '';
 
-  buildInputs = [ pytest case ];
+  checkInputs = [ pytest_32 case ];
   propagatedBuildInputs = [ kombu billiard pytz anyjson amqp eventlet ];
 
   meta = with stdenv.lib; {
diff --git a/pkgs/development/python-modules/cement/default.nix b/pkgs/development/python-modules/cement/default.nix
index 9b744957540..16b74913b7b 100644
--- a/pkgs/development/python-modules/cement/default.nix
+++ b/pkgs/development/python-modules/cement/default.nix
@@ -1,18 +1,20 @@
-{ stdenv, buildPythonPackage, fetchPypi }:
+{ stdenv, buildPythonPackage, fetchPypi, isPy3k }:
 
 buildPythonPackage rec {
   pname = "cement";
-  version = "2.10.12";
+  version = "3.0.0";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "58efb4eacd9ec977ce797a364a13851de6e42392bbde5287d44294f06c5a2f70";
+    sha256 = "e50e1033d61d18b36787a60d52cad0d3fe20780e7e2f78f0204bde32000645f9";
   };
 
   # Disable test tests since they depend on a memcached server running on
   # 127.0.0.1:11211.
   doCheck = false;
 
+  disabled = !isPy3k;
+
   meta = with stdenv.lib; {
     homepage = http://builtoncement.com/;
     description = "A CLI Application Framework for Python.";
diff --git a/pkgs/development/python-modules/certifi/default.nix b/pkgs/development/python-modules/certifi/default.nix
index 3bc686121cf..40b3338fdec 100644
--- a/pkgs/development/python-modules/certifi/default.nix
+++ b/pkgs/development/python-modules/certifi/default.nix
@@ -5,11 +5,11 @@
 
 buildPythonPackage rec {
   pname = "certifi";
-  version = "2018.4.16";
+  version = "2018.8.24";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "13e698f54293db9f89122b0581843a782ad0934a4fe0172d2a980ba77fc61bb7";
+    sha256 = "376690d6f16d32f9d1fe8932551d80b23e9d393a8578c5633a2ed39a64861638";
   };
 
   meta = {
diff --git a/pkgs/development/python-modules/cftime/default.nix b/pkgs/development/python-modules/cftime/default.nix
index 425a53987ca..9190f274a24 100644
--- a/pkgs/development/python-modules/cftime/default.nix
+++ b/pkgs/development/python-modules/cftime/default.nix
@@ -9,11 +9,11 @@
 
 buildPythonPackage rec {
   pname = "cftime";
-  version = "1.0.0";
+  version = "1.0.1";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "f62fe79ed2ad38f4211477e59f6f045c91278351f4ce7578e33ddf52fb121ea8";
+    sha256 = "20556931f546838d09be5d589482dfae6164e0d403f0aab2163c006b680d3b92";
   };
 
   checkInputs = [ pytest coveralls pytestcov ];
diff --git a/pkgs/development/python-modules/chainer/default.nix b/pkgs/development/python-modules/chainer/default.nix
index d332d99cf80..d0467888a88 100644
--- a/pkgs/development/python-modules/chainer/default.nix
+++ b/pkgs/development/python-modules/chainer/default.nix
@@ -6,11 +6,11 @@
 
 buildPythonPackage rec {
   pname = "chainer";
-  version = "4.3.0";
+  version = "4.4.0";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "a83044256edb1946c47cb9ae687d195c2aa0deaef46ab85a8ffc4a01f7001683";
+    sha256 = "9cc4d43e1ea3e0766e211e4e755dbb879f2cf27a805cfa52e32b99fd1e5f24dd";
   };
 
   checkInputs = [
diff --git a/pkgs/development/python-modules/channels/default.nix b/pkgs/development/python-modules/channels/default.nix
index c63fe87dedc..cdcfc72000d 100644
--- a/pkgs/development/python-modules/channels/default.nix
+++ b/pkgs/development/python-modules/channels/default.nix
@@ -3,11 +3,11 @@
 }:
 buildPythonPackage rec {
   pname = "channels";
-  version = "2.1.2";
+  version = "2.1.3";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "173441ccf2ac3a93c3b4f86135db301cbe95be58f5815c1e071f2e7154c192a2";
+    sha256 = "8d503d18b92cef488ba68808a2205e055d29a6a1abae92d277f8f7a9c8752f13";
   };
 
   # Files are missing in the distribution
diff --git a/pkgs/development/python-modules/cherrypy/default.nix b/pkgs/development/python-modules/cherrypy/default.nix
index e9ae4bde8cc..cb3c48c0882 100644
--- a/pkgs/development/python-modules/cherrypy/default.nix
+++ b/pkgs/development/python-modules/cherrypy/default.nix
@@ -1,20 +1,20 @@
 { lib, buildPythonPackage, fetchPypi
-, cheroot, portend, routes, six
-, setuptools_scm
+, cheroot, contextlib2, portend, routes, six
+, setuptools_scm, zc_lockfile
 , backports_unittest-mock, objgraph, pathpy, pytest, pytestcov
 , backports_functools_lru_cache, requests_toolbelt
 }:
 
 buildPythonPackage rec {
   pname = "CherryPy";
-  version = "17.0.0";
+  version = "17.3.0";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "3cdb5fbae183db49ab1f1a90643d521aa060c93f90001cc99c19d8d15b7a3fb7";
+    sha256 = "c3e4d76232ade4c47666b9008f92556465df517b8dca833ece3bed027028ae7d";
   };
 
-  propagatedBuildInputs = [ cheroot portend routes six ];
+  propagatedBuildInputs = [ cheroot contextlib2 portend routes six zc_lockfile ];
 
   buildInputs = [ setuptools_scm ];
 
diff --git a/pkgs/development/python-modules/cloudpickle/default.nix b/pkgs/development/python-modules/cloudpickle/default.nix
index acae5d73b2c..f70ebee411a 100644
--- a/pkgs/development/python-modules/cloudpickle/default.nix
+++ b/pkgs/development/python-modules/cloudpickle/default.nix
@@ -2,11 +2,11 @@
 
 buildPythonPackage rec {
   pname = "cloudpickle";
-  version = "0.5.3";
+  version = "0.5.5";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "54858c7b7dc763ed894ff91059c1d0b017d593fe23850d3d8d75f47d98398197";
+    sha256 = "6ea4b548f61a4f616b065182716318c7dced8c053517f35ac59cec22802daf3d";
   };
 
   buildInputs = [ pytest mock ];
diff --git a/pkgs/development/python-modules/cmd2/default.nix b/pkgs/development/python-modules/cmd2/default.nix
index 1997c2389ab..4217d193cfe 100644
--- a/pkgs/development/python-modules/cmd2/default.nix
+++ b/pkgs/development/python-modules/cmd2/default.nix
@@ -1,15 +1,15 @@
 { stdenv, fetchPypi, buildPythonPackage, pythonOlder, isPy3k
 , pyperclip, six, pyparsing, vim, wcwidth, colorama
-, contextlib2 ? null
+, contextlib2 ? null, setuptools_scm
 , pytest, mock, which, glibcLocales
 }:
 buildPythonPackage rec {
   pname = "cmd2";
-  version = "0.9.3";
+  version = "0.9.4";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "cffc94ad46425f80dfb243f53f456b11cea3f45e683504a60b64618a6d28b417";
+    sha256 = "0037dcf92331c63ae43e7e644536e646fff8be2fd5a83da06b3482f910f929c6";
   };
 
   LC_ALL="en_US.UTF-8";
@@ -31,6 +31,10 @@ buildPythonPackage rec {
   doCheck = !stdenv.isDarwin;
   disabled = !isPy3k;
 
+  buildInputs = [
+    setuptools_scm
+  ];
+
   propagatedBuildInputs = [
     colorama
     pyperclip
diff --git a/pkgs/development/python-modules/coveralls/default.nix b/pkgs/development/python-modules/coveralls/default.nix
index f57e0fe8609..d0e26e2e07a 100644
--- a/pkgs/development/python-modules/coveralls/default.nix
+++ b/pkgs/development/python-modules/coveralls/default.nix
@@ -16,12 +16,12 @@
 buildPythonPackage rec {
   pname = "coveralls";
   name = "${pname}-python-${version}";
-  version = "1.3.0";
+  version = "1.4.0";
 
   # wanted by tests
   src = fetchPypi {
     inherit pname version;
-    sha256 = "664794748d2e5673e347ec476159a9d87f43e0d2d44950e98ed0e27b98da8346";
+    sha256 = "7ddb2e3114db9604a7cb1fcc68a7dcca32dce346f5ba568c99979b38e166f5a6";
   };
 
   checkInputs = [
diff --git a/pkgs/development/python-modules/cryptography/default.nix b/pkgs/development/python-modules/cryptography/default.nix
index 52244ae4d96..2771e74e134 100644
--- a/pkgs/development/python-modules/cryptography/default.nix
+++ b/pkgs/development/python-modules/cryptography/default.nix
@@ -23,11 +23,11 @@
 buildPythonPackage rec {
   # also bump cryptography_vectors
   pname = "cryptography";
-  version = "2.3";
+  version = "2.3.1";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "c132bab45d4bd0fff1d3fe294d92b0a6eb8404e93337b3127bdec9f21de117e6";
+    sha256 = "8d10113ca826a4c29d5b85b2c4e045ffa8bad74fb525ee0eceb1d38d4c70dfd6";
   };
 
   outputs = [ "out" "dev" ];
diff --git a/pkgs/development/python-modules/cryptography_vectors/default.nix b/pkgs/development/python-modules/cryptography_vectors/default.nix
index ba896d29fc5..bcb60eb0d8d 100644
--- a/pkgs/development/python-modules/cryptography_vectors/default.nix
+++ b/pkgs/development/python-modules/cryptography_vectors/default.nix
@@ -5,11 +5,11 @@
 buildPythonPackage rec {
   # also bump cryptography
   pname = "cryptography_vectors";
-  version = "2.3";
+  version = "2.3.1";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "356a2ded84ae379e556515eec9b68dd74957651a38465d10605bb9fbae280f15";
+    sha256 = "bf4d9b61dce69c49e830950aa36fad194706463b0b6dfe81425b9e0bc6644d46";
   };
 
   # No tests included
diff --git a/pkgs/development/python-modules/cupy/default.nix b/pkgs/development/python-modules/cupy/default.nix
index 5d9ae10b09a..9a836e88752 100644
--- a/pkgs/development/python-modules/cupy/default.nix
+++ b/pkgs/development/python-modules/cupy/default.nix
@@ -6,11 +6,11 @@
 
 buildPythonPackage rec {
   pname = "cupy";
-  version = "4.3.0";
+  version = "4.4.0";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "ea818ff7f36cf6e5b3d3faef5af36a501c8bdeb78805820afa2999789ed698d5";
+    sha256 = "fca0e3d3fdad4c825197ea421bed0d253224b44daf738d82af5cba856c1c0b3e";
   };
 
   checkInputs = [
diff --git a/pkgs/development/python-modules/debian/default.nix b/pkgs/development/python-modules/debian/default.nix
index e4cd21bce4a..f09195b6dc5 100644
--- a/pkgs/development/python-modules/debian/default.nix
+++ b/pkgs/development/python-modules/debian/default.nix
@@ -1,14 +1,22 @@
-{ buildPythonPackage, fetchPypi
+{ lib, buildPythonPackage, fetchPypi
 , chardet, six}:
 
 buildPythonPackage rec {
   pname = "python-debian";
-  version = "0.1.32";
+  version = "0.1.33";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "143887ac647ad30819f289f5a4ca13b77e56df27b686b84c34669447f7591280";
+    sha256 = "06e91d45019fe5f2e111ba827ea77730d6ce2fea698ada4e5b0b70b5fdbc18c5";
   };
 
   propagatedBuildInputs = [ chardet six ];
+
+  # No tests in archive
+  doCheck = false;
+
+  meta = {
+    description = "Debian package related modules";
+    license = lib.licenses.gpl2;
+  };
 }
diff --git a/pkgs/development/python-modules/deform/default.nix b/pkgs/development/python-modules/deform/default.nix
index 53286b38722..3951558cf27 100644
--- a/pkgs/development/python-modules/deform/default.nix
+++ b/pkgs/development/python-modules/deform/default.nix
@@ -4,11 +4,11 @@
 
 buildPythonPackage rec {
   pname = "deform";
-  version = "2.0.5";
+  version = "2.0.6";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "874d3346a02c500432efdcc73b1a7174aa0ea69cd52a99bb9a812967f54f6f79";
+    sha256 = "bda0b809c8a668e105e30650a6766103207eafdd12c313acd59274ccd2c4d297";
   };
 
   postPatch = ''
diff --git a/pkgs/development/python-modules/detox/default.nix b/pkgs/development/python-modules/detox/default.nix
index 7c3aa87e9b8..3e2c814292b 100644
--- a/pkgs/development/python-modules/detox/default.nix
+++ b/pkgs/development/python-modules/detox/default.nix
@@ -3,11 +3,11 @@
 
 buildPythonPackage rec {
   pname = "detox";
-  version = "0.12";
+  version = "0.13";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "06svvkszg6xlg0fr471smn4rmpfga960d6qqsyhyiwa48k59n4gk";
+    sha256 = "f0c2af9c29f8e200a50b561ccc531df3087c80e7d3de6cfa9828f5fea3c8f56c";
   };
 
   buildInputs = [ pytest ];
diff --git a/pkgs/development/python-modules/dftfit/default.nix b/pkgs/development/python-modules/dftfit/default.nix
new file mode 100644
index 00000000000..01bd23c4b6f
--- /dev/null
+++ b/pkgs/development/python-modules/dftfit/default.nix
@@ -0,0 +1,47 @@
+{ lib
+, fetchPypi
+, buildPythonPackage
+, pymatgen
+, marshmallow
+, pyyaml
+, pygmo
+, pandas
+, scipy
+, numpy
+, scikitlearn
+, lammps-cython
+, pymatgen-lammps
+, pytestrunner
+, pytest
+, pytestcov
+, pytest-benchmark
+, isPy3k
+, openssh
+}:
+
+buildPythonPackage rec {
+  pname = "dftfit";
+  version = "0.4.22";
+  disabled = (!isPy3k);
+
+  src = fetchPypi {
+     inherit pname version;
+     sha256 = "06dbdc21cf9ed199bfceae5301172bee2164a3b9ef6f0814a089530c320ebb3a";
+  };
+
+  buildInputs = [ pytestrunner ];
+  checkInputs = [ pytest pytestcov pytest-benchmark openssh ];
+  propagatedBuildInputs = [ pymatgen marshmallow pyyaml pygmo
+                            pandas scipy numpy scikitlearn
+                            lammps-cython pymatgen-lammps ];
+
+  # tests require git lfs download. and is quite large so skip tests
+  doCheck = false;
+
+  meta = {
+    description = "Ab-Initio Molecular Dynamics Potential Development";
+    homepage = https://gitlab.com/costrouc/dftfit;
+    license = lib.licenses.mit;
+    maintainers = with lib.maintainers; [ costrouc ];
+  };
+}
diff --git a/pkgs/development/python-modules/docker/default.nix b/pkgs/development/python-modules/docker/default.nix
index dd4aafe1aa9..85c2a4b0230 100644
--- a/pkgs/development/python-modules/docker/default.nix
+++ b/pkgs/development/python-modules/docker/default.nix
@@ -3,12 +3,12 @@
 , ipaddress, backports_ssl_match_hostname, docker_pycreds
 }:
 buildPythonPackage rec {
-  version = "3.4.1";
+  version = "3.5.0";
   pname = "docker";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "ad077b49660b711d20f50f344f70cfae014d635ef094bf21b0d7df5f0aeedf99";
+    sha256 = "bc693be5a84b3b9e5aaf156068c5c0a445ee5138c638c3fbc857133bf67ebe07";
   };
 
   propagatedBuildInputs = [
diff --git a/pkgs/development/python-modules/docutils/default.nix b/pkgs/development/python-modules/docutils/default.nix
new file mode 100644
index 00000000000..c31cfceebba
--- /dev/null
+++ b/pkgs/development/python-modules/docutils/default.nix
@@ -0,0 +1,35 @@
+{ lib
+, fetchurl
+, buildPythonPackage
+, isPy3k
+, python
+}:
+
+buildPythonPackage rec {
+  pname = "docutils";
+  version = "0.14";
+
+  src = fetchurl {
+    url = "mirror://sourceforge/docutils/${pname}.tar.gz";
+    sha256 = "0x22fs3pdmr42kvz6c654756wja305qv6cx1zbhwlagvxgr4xrji";
+  };
+
+  checkPhase = if isPy3k then ''
+    ${python.interpreter} test3/alltests.py
+  '' else ''
+    ${python.interpreter} test/alltests.py
+  '';
+
+  # Create symlinks lacking a ".py" suffix, many programs depend on these names
+  postFixup = ''
+    (cd $out/bin && for f in *.py; do
+      ln -s $f $(echo $f | sed -e 's/\.py$//')
+    done)
+  '';
+
+  meta = {
+    description = "Docutils -- Python Documentation Utilities";
+    homepage = http://docutils.sourceforge.net/;
+    maintainers = with lib.maintainers; [ garbas AndersonTorres ];
+  };
+}
diff --git a/pkgs/development/python-modules/dogpile.cache/default.nix b/pkgs/development/python-modules/dogpile.cache/default.nix
index 9a840e5112a..b830d34589b 100644
--- a/pkgs/development/python-modules/dogpile.cache/default.nix
+++ b/pkgs/development/python-modules/dogpile.cache/default.nix
@@ -4,11 +4,11 @@
 
 buildPythonPackage rec {
   pname = "dogpile.cache";
-  version = "0.6.6";
+  version = "0.6.7";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "044d4ea0a0abc72491044f3d3df8e1fc9e8fa7a436c6e9a0da5850d23a0d16c1";
+    sha256 = "fca7deb7c276b879b01c15c5d39b3c05701dc43b263ec3fef1e52cb851cf88ab";
   };
 
   # Disable concurrency tests that often fail,
diff --git a/pkgs/development/python-modules/dulwich/default.nix b/pkgs/development/python-modules/dulwich/default.nix
index 2617249b75a..4713ff0ab28 100644
--- a/pkgs/development/python-modules/dulwich/default.nix
+++ b/pkgs/development/python-modules/dulwich/default.nix
@@ -4,12 +4,12 @@
 , git, glibcLocales }:
 
 buildPythonPackage rec {
-  version = "0.19.5";
+  version = "0.19.6";
   pname = "dulwich";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "34f99e575fe1f1e89cca92cec1ddd50b4991199cb00609203b28df9eb83ce259";
+    sha256 = "9a7dc5c5759f3d3b7a9ac0a684aa2c47f099e1722d9caab5b043cef1d73ff4a2";
   };
 
   LC_ALL = "en_US.UTF-8";
diff --git a/pkgs/development/python-modules/easydict/default.nix b/pkgs/development/python-modules/easydict/default.nix
index eb98cd18ef2..aed91033e97 100644
--- a/pkgs/development/python-modules/easydict/default.nix
+++ b/pkgs/development/python-modules/easydict/default.nix
@@ -2,11 +2,11 @@
 
 buildPythonPackage rec {
   pname = "easydict";
-  version = "1.7";
+  version = "1.8";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "1xpnwjdw4x5kficjgcajqcal6bxcb0ax8l6hdkww9fp6lrh28x8v";
+    sha256 = "f1ec91110737a62fe28d14970ffa7a7c7b441a32e35a6f3da6a6082ffb7f9432";
   };
 
   docheck = false; # No tests in archive
diff --git a/pkgs/development/python-modules/elasticsearch/default.nix b/pkgs/development/python-modules/elasticsearch/default.nix
index 087ca3910c5..6c5ab07db19 100644
--- a/pkgs/development/python-modules/elasticsearch/default.nix
+++ b/pkgs/development/python-modules/elasticsearch/default.nix
@@ -7,11 +7,11 @@
 
 buildPythonPackage (rec {
   pname = "elasticsearch";
-  version = "6.3.0";
+  version = "6.3.1";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "80ff7a1a56920535a9987da333c7e385b2ded27595b6de33860707dab758efbe";
+    sha256 = "aada5cfdc4a543c47098eb3aca6663848ef5d04b4324935ced441debc11ec98b";
   };
 
   # Check is disabled because running them destroy the content of the local cluster!
diff --git a/pkgs/development/python-modules/faker/default.nix b/pkgs/development/python-modules/faker/default.nix
index 74ed13da8b4..93337aa8d18 100644
--- a/pkgs/development/python-modules/faker/default.nix
+++ b/pkgs/development/python-modules/faker/default.nix
@@ -8,11 +8,11 @@ assert pythonOlder "3.3" -> ipaddress != null;
 
 buildPythonPackage rec {
   pname = "Faker";
-  version = "0.8.17";
+  version = "0.8.18";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "0e9a1227a3a0f3297a485715e72ee6eb77081b17b629367042b586e38c03c867";
+    sha256 = "0184fa252f86214308bb6bed344f96294f2e3528fbffafc727890cf2a86d6027";
   };
 
   checkInputs = [
diff --git a/pkgs/development/python-modules/fastrlock/default.nix b/pkgs/development/python-modules/fastrlock/default.nix
index 848f01d6e16..9b553e65db6 100644
--- a/pkgs/development/python-modules/fastrlock/default.nix
+++ b/pkgs/development/python-modules/fastrlock/default.nix
@@ -2,11 +2,11 @@
 
 buildPythonPackage rec {
   pname = "fastrlock";
-  version = "0.3";
+  version = "0.4";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "00mr9b15d539z89ng5nf89s2ryhk90xwx95jal77ma0wslixrk5d";
+    sha256 = "6abdbb35205792e2d2a8c441aaa41a613d43ee2d88b3af4fd9735ae7a5f7db6b";
   };
 
   meta = with stdenv.lib; {
diff --git a/pkgs/development/python-modules/filelock/default.nix b/pkgs/development/python-modules/filelock/default.nix
index 46d26e80d56..cfa0e1be74f 100644
--- a/pkgs/development/python-modules/filelock/default.nix
+++ b/pkgs/development/python-modules/filelock/default.nix
@@ -2,11 +2,11 @@
 
 buildPythonPackage rec {
   pname = "filelock";
-  version = "3.0.4";
+  version = "3.0.6";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "011327d4ed939693a5b28c0fdf2fd9bda1f68614c1d6d0643a89382ce9843a71";
+    sha256 = "59ccab92fe118da7e5ce5a9fcd95506ade58d9d5f606db4922192524edfac820";
   };
 
   meta = with stdenv.lib; {
diff --git a/pkgs/development/python-modules/folium/default.nix b/pkgs/development/python-modules/folium/default.nix
index 9cef17dc772..7ff4a37d6d3 100644
--- a/pkgs/development/python-modules/folium/default.nix
+++ b/pkgs/development/python-modules/folium/default.nix
@@ -18,10 +18,10 @@ buildPythonPackage rec {
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "0yfb8ygq67m149n72bb8h7dk9mx8d3ivc5ygqwdj4q8qggj1ns08";
+    sha256 = "08681be47b1861221bc7cf17b6e368a8d734db81682d716c22a11e839f47cb79";
   };
 
-  checkInputs = [ pytest numpy nbconvert pandas mock ];
+  checkInputs = [ pytest nbconvert pandas mock ];
   propagatedBuildInputs = [ jinja2 branca six requests numpy ];
 
   # No tests in archive
diff --git a/pkgs/development/python-modules/fonttools/default.nix b/pkgs/development/python-modules/fonttools/default.nix
index 4874fbba3c6..4759e9d3c83 100644
--- a/pkgs/development/python-modules/fonttools/default.nix
+++ b/pkgs/development/python-modules/fonttools/default.nix
@@ -8,11 +8,11 @@
 
 buildPythonPackage rec {
   pname = "fonttools";
-  version = "3.28.0";
+  version = "3.29.0";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "ebf2ee25a6060e8551880a3b05d6ecadcdcfbd1b32fc272ff7b3acdb22945b6f";
+    sha256 = "aab38c8c131670684321437d4857dcb4de1c775efd152a9ca9c4d81f1cb97fe7";
     extension = "zip";
   };
 
diff --git a/pkgs/development/python-modules/gevent/default.nix b/pkgs/development/python-modules/gevent/default.nix
index cd28a4976a9..50953fd7d3f 100644
--- a/pkgs/development/python-modules/gevent/default.nix
+++ b/pkgs/development/python-modules/gevent/default.nix
@@ -2,11 +2,11 @@
 
 buildPythonPackage rec {
   pname = "gevent";
-  version = "1.3.5";
+  version = "1.3.6";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "7f15861f3cc92f49663ca88c4774d26d8044783a65fbc28071a2bd1c7bf36ff0";
+    sha256 = "7b413c391e8ad6607b7f7540d698a94349abd64e4935184c595f7cdcc69904c6";
   };
 
   buildInputs = [ libev ];
diff --git a/pkgs/development/python-modules/google_api_core/default.nix b/pkgs/development/python-modules/google_api_core/default.nix
index 2273b48b5b3..ded728bdc0d 100644
--- a/pkgs/development/python-modules/google_api_core/default.nix
+++ b/pkgs/development/python-modules/google_api_core/default.nix
@@ -3,11 +3,11 @@
 
 buildPythonPackage rec {
   pname = "google-api-core";
-  version = "1.2.1";
+  version = "1.3.0";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "e24e391054ed6e925ff6d03f225d9f66f3da97d0ab6f61e59274fb918fbe3ef1";
+    sha256 = "ac85fc7f6687bb0271f2f70ca298da90f35789f9de1fe3a11e8caeb571332b77";
   };
 
   propagatedBuildInputs = [
diff --git a/pkgs/development/python-modules/google_auth/default.nix b/pkgs/development/python-modules/google_auth/default.nix
index d908bb04151..fde773e738b 100644
--- a/pkgs/development/python-modules/google_auth/default.nix
+++ b/pkgs/development/python-modules/google_auth/default.nix
@@ -3,11 +3,11 @@
 
 buildPythonPackage rec {
   pname = "google-auth";
-  version = "1.5.0";
+  version = "1.5.1";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "1745c9066f698eac3da99cef082914495fb71bc09597ba7626efbbb64c4acc57";
+    sha256 = "9ca363facbf2622d9ba828017536ccca2e0f58bd15e659b52f312172f8815530";
   };
 
   checkInputs = [ pytest mock oauth2client flask requests urllib3 pytest-localserver ];
diff --git a/pkgs/development/python-modules/gphoto2/default.nix b/pkgs/development/python-modules/gphoto2/default.nix
index 29aa0400ec5..9757cb950dc 100644
--- a/pkgs/development/python-modules/gphoto2/default.nix
+++ b/pkgs/development/python-modules/gphoto2/default.nix
@@ -4,11 +4,11 @@
 
 buildPythonPackage rec {
   pname = "gphoto2";
-  version = "1.8.2";
+  version = "1.8.3";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "1806bdjc18qh0wyayxymgjnqqqlxs2iwvgk594anxw9y69hrxqni";
+    sha256 = "0257f90f0d8342b8bc996ff1b45b2cd3219a29f8123aa21a6da159ee3566e49f";
   };
 
   nativeBuildInputs = [ pkgconfig ];
diff --git a/pkgs/development/python-modules/grpcio-tools/default.nix b/pkgs/development/python-modules/grpcio-tools/default.nix
index 8d4c925acf8..c111e5f75a7 100644
--- a/pkgs/development/python-modules/grpcio-tools/default.nix
+++ b/pkgs/development/python-modules/grpcio-tools/default.nix
@@ -2,11 +2,11 @@
 
 buildPythonPackage rec {
   pname = "grpcio-tools";
-  version = "1.13.0";
+  version = "1.14.1";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "1ck6818kb4nb6skm9lqg492brqs7kfk65f4hh2c7h7c8pkbrpcw1";
+    sha256 = "4ce5aa660d7884f23aac1eafa93b97a4c3e2b512edff871e91fdb6ee86ebd5ea";
   };
 
   enableParallelBuilding = true;
diff --git a/pkgs/development/python-modules/grpcio/default.nix b/pkgs/development/python-modules/grpcio/default.nix
index 204080fe115..3d3824cdabe 100644
--- a/pkgs/development/python-modules/grpcio/default.nix
+++ b/pkgs/development/python-modules/grpcio/default.nix
@@ -4,11 +4,11 @@
 with stdenv.lib;
 buildPythonPackage rec {
   pname = "grpcio";
-  version = "1.13.0";
+  version = "1.14.1";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "6324581e215157f0fbe335dff2e21a65b4406db98ac7cca05f1e23b4f510b426";
+    sha256 = "4bf23666e763ca7ff6010465864e9f088f4ac7ecc1e11abd6f85b250e66b2c05";
   };
 
   nativeBuildInputs = [ pkgconfig ] ++ optional stdenv.isDarwin darwin.cctools;
diff --git a/pkgs/development/python-modules/h5py/default.nix b/pkgs/development/python-modules/h5py/default.nix
index 2b95b1473cb..01c33117849 100644
--- a/pkgs/development/python-modules/h5py/default.nix
+++ b/pkgs/development/python-modules/h5py/default.nix
@@ -37,6 +37,9 @@ in buildPythonPackage rec {
   propagatedBuildInputs = [ numpy six]
     ++ optionals mpiSupport [ mpi4py openssh ];
 
+  # https://github.com/h5py/h5py/issues/1088
+  doCheck = false;
+
   meta = {
     description =
       "Pythonic interface to the HDF5 binary data format";
diff --git a/pkgs/development/python-modules/hvac/default.nix b/pkgs/development/python-modules/hvac/default.nix
index f18d8eadec8..310bd91b22b 100644
--- a/pkgs/development/python-modules/hvac/default.nix
+++ b/pkgs/development/python-modules/hvac/default.nix
@@ -2,11 +2,11 @@
 
 buildPythonPackage rec {
   pname = "hvac";
-  version = "0.6.2";
+  version = "0.6.3";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "4bc80744df5f09882b1cc91755b03b7b62b093fc63c8c4abb26fbfb9c9e878dd";
+    sha256 = "54672a93f75453a7de13c7c10c6d8a51630e2559a8e2a563d8e272e9e188443f";
   };
 
   propagatedBuildInputs = [ requests ];
diff --git a/pkgs/development/python-modules/ibmquantumexperience/default.nix b/pkgs/development/python-modules/ibmquantumexperience/default.nix
index 0fcb2662801..82f6cb144ac 100644
--- a/pkgs/development/python-modules/ibmquantumexperience/default.nix
+++ b/pkgs/development/python-modules/ibmquantumexperience/default.nix
@@ -7,11 +7,11 @@
 
 buildPythonPackage rec {
   pname = "IBMQuantumExperience";
-  version = "1.9.8";
+  version = "2.0.2";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "78a7d9770fa2884d79d3c8b18f374644866e4d22ec151cf703053f7530bb7b7c";
+    sha256 = "f2a5662d7457c297af0751985979e64a88569beb07cfedad0ce1dfa5a7237842";
   };
 
   propagatedBuildInputs = [
diff --git a/pkgs/development/python-modules/invoke/default.nix b/pkgs/development/python-modules/invoke/default.nix
index 20d2973ca4f..8785f1fa6db 100644
--- a/pkgs/development/python-modules/invoke/default.nix
+++ b/pkgs/development/python-modules/invoke/default.nix
@@ -5,11 +5,11 @@
 
 buildPythonPackage rec {
   pname = "invoke";
-  version = "1.1.0";
+  version = "1.1.1";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "0aiy1xvk1f91246zxd1zqrm679vdvd10h843a2na41cqr3cflpi6";
+    sha256 = "1c2cf54c9b9af973ad9704d8ba81b225117cab612568cacbfb3fc42958cc20a9";
   };
 
   # errors with vendored libs
diff --git a/pkgs/development/python-modules/ipython/default.nix b/pkgs/development/python-modules/ipython/default.nix
index 2c0e4aaf4db..efc6933807f 100644
--- a/pkgs/development/python-modules/ipython/default.nix
+++ b/pkgs/development/python-modules/ipython/default.nix
@@ -23,11 +23,11 @@
 
 buildPythonPackage rec {
   pname = "ipython";
-  version = "6.4.0";
+  version = "6.5.0";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "eca537aa61592aca2fef4adea12af8e42f5c335004dfa80c78caf80e8b525e5c";
+    sha256 = "b0f2ef9eada4a68ef63ee10b6dde4f35c840035c50fd24265f8052c98947d5a4";
   };
 
   prePatch = lib.optionalString stdenv.isDarwin ''
diff --git a/pkgs/development/python-modules/ipywidgets/default.nix b/pkgs/development/python-modules/ipywidgets/default.nix
index 9f15a2fc5c2..dde041140b9 100644
--- a/pkgs/development/python-modules/ipywidgets/default.nix
+++ b/pkgs/development/python-modules/ipywidgets/default.nix
@@ -14,11 +14,11 @@
 
 buildPythonPackage rec {
   pname = "ipywidgets";
-  version = "7.3.0";
+  version = "7.4.0";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "3ce93db970a94f06f38121da70757cdbcce884ecd14f79a4dd9bc49a47e0f33b";
+    sha256 = "fd24a66d82f2ea49e281da7714a7c656340d3ec24dff376b17590fa59469b817";
   };
 
   # Tests are not distributed
diff --git a/pkgs/development/python-modules/jdatetime/default.nix b/pkgs/development/python-modules/jdatetime/default.nix
index db79050077f..a7c362231ca 100644
--- a/pkgs/development/python-modules/jdatetime/default.nix
+++ b/pkgs/development/python-modules/jdatetime/default.nix
@@ -2,11 +2,11 @@
 
 buildPythonPackage rec {
   pname = "jdatetime";
-  version = "2.2.1";
+  version = "3.0.0";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "030a47ad3acbde45cb03872e2c6415c675dbb4a82462302971e93076145b5096";
+    sha256 = "07cdb02e8d6610c38e8ae7746b12cbc39068cc5d54fb2baa915579b60d781b5b";
   };
 
   propagatedBuildInputs = [ six ];
diff --git a/pkgs/development/python-modules/jinja2/default.nix b/pkgs/development/python-modules/jinja2/default.nix
index 7432b3bb99c..b800303c20c 100644
--- a/pkgs/development/python-modules/jinja2/default.nix
+++ b/pkgs/development/python-modules/jinja2/default.nix
@@ -14,9 +14,12 @@ buildPythonPackage rec {
   propagatedBuildInputs = [ markupsafe ];
 
   checkPhase = ''
-    pytest -v
+    pytest -v tests
   '';
 
+  # RecursionError: maximum recursion depth exceeded
+  doCheck = false;
+
   meta = with stdenv.lib; {
     homepage = http://jinja.pocoo.org/;
     description = "Stand-alone template engine";
diff --git a/pkgs/development/python-modules/jira/default.nix b/pkgs/development/python-modules/jira/default.nix
index ac4f45f4e9d..b9bc923e7e0 100644
--- a/pkgs/development/python-modules/jira/default.nix
+++ b/pkgs/development/python-modules/jira/default.nix
@@ -6,13 +6,13 @@
 
 buildPythonPackage rec {
   pname = "jira";
-  version = "1.0.15";
+  version = "2.0.0";
 
   PBR_VERSION = version;
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "20108a1d5b0dd058d5d4e0047f2d09ee06aaa413b22ca4d5c249e86167417fe8";
+    sha256 = "e2a94adff98e45b29ded030adc76103eab34fa7d4d57303f211f572bedba0e93";
   };
 
   buildInputs = [ glibcLocales pytest pytestcov pytestrunner pbr ];
diff --git a/pkgs/development/python-modules/joblib/default.nix b/pkgs/development/python-modules/joblib/default.nix
index 8b42e6e1ea1..7164fd1197b 100644
--- a/pkgs/development/python-modules/joblib/default.nix
+++ b/pkgs/development/python-modules/joblib/default.nix
@@ -9,10 +9,10 @@
 
 buildPythonPackage rec {
   pname = "joblib";
-  version = "0.12.1";
+  version = "0.12.3";
   src = fetchPypi {
     inherit pname version;
-    sha256 = "68e6128e4734196616a39e2d48830ec7d61551c7f5748849e4c91478d2444524";
+    sha256 = "333b9bf16ff015d6b56bf80b9831afdd243443cb84c7ff7b6e342f117e354c42";
   };
 
   checkInputs = [ sphinx numpydoc pytest ];
diff --git a/pkgs/development/python-modules/jsonrpc-async/default.nix b/pkgs/development/python-modules/jsonrpc-async/default.nix
index 758fc0f1dd5..5b7ce3c12bf 100644
--- a/pkgs/development/python-modules/jsonrpc-async/default.nix
+++ b/pkgs/development/python-modules/jsonrpc-async/default.nix
@@ -3,11 +3,11 @@
 
 buildPythonPackage rec {
   pname = "jsonrpc-async";
-  version = "1.0.0";
+  version = "1.0.1";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "6241a221b52e18265fe6bb59c60633acebb6fb5ef8c04de9a076b757aa133b86";
+    sha256 = "adda3ff6e122b1932b6e20cf583666ea65db4248bc19b04811a4ccc0f0b03d95";
   };
 
   propagatedBuildInputs = [ aiohttp jsonrpc-base ];
diff --git a/pkgs/development/python-modules/jsonrpc-base/default.nix b/pkgs/development/python-modules/jsonrpc-base/default.nix
index d68b031d517..35244e092da 100644
--- a/pkgs/development/python-modules/jsonrpc-base/default.nix
+++ b/pkgs/development/python-modules/jsonrpc-base/default.nix
@@ -2,11 +2,11 @@
 
 buildPythonPackage rec {
   pname = "jsonrpc-base";
-  version = "1.0.1";
+  version = "1.0.2";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "21f860c915617f6475aa1ac5a1ec11de03cce6b279741f25ad97d8a4c5b76c3c";
+    sha256 = "f9baac32aa51c3052d03b86ff30a9856900b8b4a4eb175f7bf2c8722520b8637";
   };
 
   propagatedBuildInputs = [ ];
diff --git a/pkgs/development/python-modules/jsonrpc-websocket/default.nix b/pkgs/development/python-modules/jsonrpc-websocket/default.nix
index c753058b093..eff4f41979a 100644
--- a/pkgs/development/python-modules/jsonrpc-websocket/default.nix
+++ b/pkgs/development/python-modules/jsonrpc-websocket/default.nix
@@ -3,11 +3,11 @@
 
 buildPythonPackage rec {
   pname = "jsonrpc-websocket";
-  version = "1.0.0";
+  version = "1.0.1";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "40949836996c0a8104e7878997d3f68bda4561e9d3af64e5cd178127ec3c2778";
+    sha256 = "e74e490fefa3b8f33620fca98f7cd9a53fb765b9ed6f78360482a3f364230885";
   };
 
   propagatedBuildInputs = [ aiohttp jsonrpc-base ];
diff --git a/pkgs/development/python-modules/junos-eznc/default.nix b/pkgs/development/python-modules/junos-eznc/default.nix
index f72bec57e90..fb34f4696ee 100644
--- a/pkgs/development/python-modules/junos-eznc/default.nix
+++ b/pkgs/development/python-modules/junos-eznc/default.nix
@@ -15,11 +15,11 @@
 
 buildPythonPackage rec {
   pname = "junos-eznc";
-  version = "2.1.8";
+  version = "2.1.9";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "daa62e5abfc66ef12e4fb43a1c264673e662e6f2d937cd10666c1c6dcf2ac6ac";
+    sha256 = "a6729c35efd764e1f22457b72898bba554986466306ad29ad2d0bb071e997093";
   };
 
 
diff --git a/pkgs/development/python-modules/jupyterlab/default.nix b/pkgs/development/python-modules/jupyterlab/default.nix
index e47fdfa15ba..23aaff8a728 100644
--- a/pkgs/development/python-modules/jupyterlab/default.nix
+++ b/pkgs/development/python-modules/jupyterlab/default.nix
@@ -1,12 +1,12 @@
 { lib, buildPythonPackage, isPy3k, fetchPypi, ipython_genutils, jupyterlab_launcher, notebook }:
 buildPythonPackage rec {
   pname = "jupyterlab";
-  version = "0.33.7";
+  version = "0.34.6";
   disabled = !isPy3k;
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "ab9f7bcbc3b4e107897f368aa0527cdc1b4ccf0c370e218ae03ac1d75fac261c";
+    sha256 = "d6e5a3855a0d55e6aa4ab704379da5da3db2e652442e79acfa2e9d14ef50ccb3";
   };
 
   propagatedBuildInputs = [
diff --git a/pkgs/development/python-modules/jupyterlab_launcher/default.nix b/pkgs/development/python-modules/jupyterlab_launcher/default.nix
index 79d22b6b1c9..1831b47ee79 100644
--- a/pkgs/development/python-modules/jupyterlab_launcher/default.nix
+++ b/pkgs/development/python-modules/jupyterlab_launcher/default.nix
@@ -1,11 +1,11 @@
 { lib, buildPythonPackage, fetchPypi, jsonschema, notebook }:
 buildPythonPackage rec {
   pname = "jupyterlab_launcher";
-  version = "0.11.2";
+  version = "0.13.1";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "236a647f4c3f8417413643a918a893a5f662fb5d2fdccce2fd101e3cca2e7fd1";
+    sha256 = "f880eada0b8b1f524d5951dc6fcae0d13b169897fc8a247d75fb5beadd69c5f0";
   };
 
   propagatedBuildInputs = [
diff --git a/pkgs/development/python-modules/keras-applications/default.nix b/pkgs/development/python-modules/keras-applications/default.nix
index e06a0b75b50..f9617f03d8e 100644
--- a/pkgs/development/python-modules/keras-applications/default.nix
+++ b/pkgs/development/python-modules/keras-applications/default.nix
@@ -2,11 +2,11 @@
 
 buildPythonPackage rec {
   pname = "Keras_Applications";
-  version = "1.0.4";
+  version = "1.0.5";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "8c95300328630ae74fb0828b6fa38269a25c0228a02f1e5181753bfd48961f49";
+    sha256 = "26a7318b9d8d5be80d75ab08a1284aaf4b94125dd8271b18ca89791e16eb2cfc";
   };
 
   # Cyclic dependency: keras-applications requires keras, which requires keras-applications
diff --git a/pkgs/development/python-modules/keras-preprocessing/default.nix b/pkgs/development/python-modules/keras-preprocessing/default.nix
index 043e43eb184..45ce1d7f61d 100644
--- a/pkgs/development/python-modules/keras-preprocessing/default.nix
+++ b/pkgs/development/python-modules/keras-preprocessing/default.nix
@@ -2,11 +2,11 @@
 
 buildPythonPackage rec {
   pname = "Keras_Preprocessing";
-  version = "1.0.2";
+  version = "1.0.3";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "f5306554d2b454d825b36f35e327744f5477bd2ae21017f1a93b2097bed6757e";
+    sha256 = "02ba0a3b31ed89c4b0c21d55ba7d87529097d56f394e3850b6d3c9e6c63ce7ae";
   };
 
   # Cyclic dependency: keras-preprocessing requires keras, which requires keras-preprocessing
diff --git a/pkgs/development/python-modules/keyrings-alt/default.nix b/pkgs/development/python-modules/keyrings-alt/default.nix
index 9f3fc8dc4d3..9564e4f3703 100644
--- a/pkgs/development/python-modules/keyrings-alt/default.nix
+++ b/pkgs/development/python-modules/keyrings-alt/default.nix
@@ -11,12 +11,15 @@ buildPythonPackage rec {
     sha256 = "0nnva8g03dv6gdhjk1ihn2qw7g15232fyj8shipah9whgfv8d75m";
   };
 
+  postPatch = ''
+    substituteInPlace pytest.ini \
+      --replace "--flake8" ""
+  '';
+
   nativeBuildInputs = [ setuptools_scm ];
   propagatedBuildInputs = [ six ];
 
-  # Fails with "ImportError: cannot import name mock"
-  #doCheck = false;
-  checkInputs = [ pytest pytest-flake8 keyring ] ++ stdenv.lib.optional (pythonOlder "3.3") backports_unittest-mock;
+  checkInputs = [ pytest keyring ] ++ stdenv.lib.optional (pythonOlder "3.3") backports_unittest-mock;
 
   checkPhase = ''
     py.test
diff --git a/pkgs/development/python-modules/kubernetes/default.nix b/pkgs/development/python-modules/kubernetes/default.nix
index 9d91fdc9679..030766eb698 100644
--- a/pkgs/development/python-modules/kubernetes/default.nix
+++ b/pkgs/development/python-modules/kubernetes/default.nix
@@ -4,7 +4,7 @@
 
 buildPythonPackage rec {
   pname = "kubernetes";
-  version = "6.0.0";
+  version = "7.0.0";
 
   prePatch = ''
     sed -e 's/sphinx>=1.2.1,!=1.3b1,<1.4 # BSD/sphinx/' -i test-requirements.txt
@@ -23,7 +23,7 @@ buildPythonPackage rec {
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "b370ab4abd925309db69a14a4723487948e9a83de60ca92782ec14992b741c89";
+    sha256 = "84dfb4319afac189e8327b71b9332b5329d2a78074f58958c5f06a870edf32ba";
   };
 
   checkInputs = [ isort coverage pytest mock sphinx autopep8 pep8 codecov recommonmark nose ];
diff --git a/pkgs/development/python-modules/lammps-cython/default.nix b/pkgs/development/python-modules/lammps-cython/default.nix
new file mode 100644
index 00000000000..501e4adc21d
--- /dev/null
+++ b/pkgs/development/python-modules/lammps-cython/default.nix
@@ -0,0 +1,53 @@
+{ lib
+, fetchurl
+, buildPythonPackage
+, lammps-mpi
+, mpi
+, mpi4py
+, numpy
+, cython
+, pymatgen
+, ase
+, pytestrunner
+, pytest
+, pytestcov
+, isPy3k
+, openssh
+}:
+
+buildPythonPackage rec {
+  pname = "lammps-cython";
+  version = "0.5.7";
+  disabled = (!isPy3k);
+
+  src = fetchurl {
+     url = "https://gitlab.com/costrouc/${pname}/-/archive/v${version}/${pname}-v${version}.tar.gz";
+     sha256 = "1wj9scmjdl00af13b5ihfccrjpikrdgkzd88ialam1nkxvxi42bl";
+  };
+
+  buildInputs = [ cython pytestrunner ];
+  checkInputs = [ pytest pytestcov openssh ];
+  propagatedBuildInputs = [ mpi4py pymatgen ase numpy ];
+
+  preBuild = ''
+    echo "Creating lammps.cfg file..."
+    cat << EOF > lammps.cfg
+    [lammps]
+    lammps_include_dir = ${lammps-mpi}/include
+    lammps_library_dir = ${lammps-mpi}/lib
+    lammps_library = lammps_mpi
+
+    [mpi]
+    mpi_include_dir = ${mpi}/include
+    mpi_library_dir = ${mpi}/lib
+    mpi_library     = mpi
+    EOF
+  '';
+
+  meta = {
+    description = "Pythonic Wrapper to LAMMPS using cython";
+    homepage = https://gitlab.com/costrouc/lammps-cython;
+    license = lib.licenses.mit;
+    maintainers = with lib.maintainers; [ costrouc ];
+  };
+}
diff --git a/pkgs/development/python-modules/ldap3/default.nix b/pkgs/development/python-modules/ldap3/default.nix
index 24690d9d530..3735cbf5852 100644
--- a/pkgs/development/python-modules/ldap3/default.nix
+++ b/pkgs/development/python-modules/ldap3/default.nix
@@ -1,12 +1,12 @@
 { stdenv, fetchPypi, buildPythonPackage, gssapi, pyasn1 }:
 
 buildPythonPackage rec {
-  version = "2.5";
+  version = "2.5.1";
   pname = "ldap3";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "55078bbc981f715a8867b4c040402627fdfccf5664e0277a621416559748e384";
+    sha256 = "cc09951809678cfb693a13a6011dd2d48ada60a52bd80cb4bd7dcc55ee7c02fd";
   };
 
   buildInputs = [ gssapi ];
diff --git a/pkgs/development/python-modules/libagent/default.nix b/pkgs/development/python-modules/libagent/default.nix
index 20312ed81d3..950a0dd5ba6 100644
--- a/pkgs/development/python-modules/libagent/default.nix
+++ b/pkgs/development/python-modules/libagent/default.nix
@@ -4,11 +4,11 @@
 
 buildPythonPackage rec {
   pname = "libagent";
-  version = "0.11.3";
+  version = "0.12.0";
 
   src = fetchPypi{
     inherit pname version;
-    sha256 = "cb6199c3572e1223756465e758fb525e7f406a4808e9d7cfdddf089bec710047";
+    sha256 = "55af1ad2a6c95aef1fc5588c2002c9e54edbb14e248776b64d00628235ceda3e";
   };
 
   buildInputs = [
diff --git a/pkgs/development/python-modules/libusb1/default.nix b/pkgs/development/python-modules/libusb1/default.nix
index f11930a3a18..245ea90038e 100644
--- a/pkgs/development/python-modules/libusb1/default.nix
+++ b/pkgs/development/python-modules/libusb1/default.nix
@@ -2,11 +2,11 @@
 
 buildPythonPackage rec {
   pname = "libusb1";
-  version = "1.6.5";
+  version = "1.6.6";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "4707f81e933a97fed1c5bf7d4957f07bae1139cb8084bdee1f50201a40e3fd7c";
+    sha256 = "a49917a2262cf7134396f6720c8be011f14aabfc5cdc53f880cc672c0f39d271";
   };
 
   postPatch = lib.optionalString stdenv.isLinux ''
diff --git a/pkgs/development/python-modules/lxml/default.nix b/pkgs/development/python-modules/lxml/default.nix
index 8589e47be21..3778098922a 100644
--- a/pkgs/development/python-modules/lxml/default.nix
+++ b/pkgs/development/python-modules/lxml/default.nix
@@ -7,11 +7,11 @@
 
 buildPythonPackage rec {
   pname = "lxml";
-  version = "4.2.3";
+  version = "4.2.4";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "622f7e40faef13d232fb52003661f2764ce6cdef3edb0a59af7c1559e4cc36d1";
+    sha256 = "e2afbe403090f5893e254958d02875e0732975e73c4c0cdd33c1f009a61963ca";
   };
 
   buildInputs = [ libxml2 libxslt ];
diff --git a/pkgs/development/python-modules/m2r/default.nix b/pkgs/development/python-modules/m2r/default.nix
index 4cb7744f3d9..8b1618515c8 100644
--- a/pkgs/development/python-modules/m2r/default.nix
+++ b/pkgs/development/python-modules/m2r/default.nix
@@ -2,11 +2,11 @@
   mistune, docutils } :
 buildPythonPackage rec {
   pname = "m2r";
-  version = "0.1.15";
+  version = "0.2.0";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "1c358d8bf21ff70e569968d604a0e3c9b05fe01b5f362389235e97bc7c0cd542";
+    sha256 = "b64ee5ac870311a69967fe787be8607df67b02a329f0fc76c8bf477336a99c78";
   };
 
   propagatedBuildInputs = [ mistune docutils ];
diff --git a/pkgs/development/python-modules/marionette-harness/mozdevice.nix b/pkgs/development/python-modules/marionette-harness/mozdevice.nix
index 491069cd87f..02da75bfd96 100644
--- a/pkgs/development/python-modules/marionette-harness/mozdevice.nix
+++ b/pkgs/development/python-modules/marionette-harness/mozdevice.nix
@@ -7,11 +7,11 @@
 
 buildPythonPackage rec {
   pname = "mozdevice";
-  version = "1.0.0";
+  version = "1.0.1";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "c3c50219127e36c171f84b2427e8fcf3a85457f336559aead9770b2a27fbc4b6";
+    sha256 = "0026241bff3ad10a73fe24eb4f59c1313c94e5950f397b2f6b8cc4e4dfbfdd73";
   };
 
   propagatedBuildInputs = [ moznetwork mozprocess ];
diff --git a/pkgs/development/python-modules/marshmallow-sqlalchemy/default.nix b/pkgs/development/python-modules/marshmallow-sqlalchemy/default.nix
index f7efeb72592..b2b0e7d4efa 100644
--- a/pkgs/development/python-modules/marshmallow-sqlalchemy/default.nix
+++ b/pkgs/development/python-modules/marshmallow-sqlalchemy/default.nix
@@ -4,7 +4,7 @@
 
 buildPythonPackage rec {
   pname = "marshmallow-sqlalchemy";
-  version = "0.14.0";
+  version = "0.14.1";
 
   meta = {
     homepage = "https://github.com/marshmallow-code/marshmallow-sqlalchemy";
@@ -14,7 +14,7 @@ buildPythonPackage rec {
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "32ff19350a8892b3e8dc954eeeac796576bb89356512f9e1ccd33da63f856930";
+    sha256 = "a42cdbd6b623059fca601e1b572cab28f00d4acf36e2cef38094c88424b3dcf1";
   };
 
   propagatedBuildInputs = [ marshmallow sqlalchemy ];
diff --git a/pkgs/development/python-modules/marshmallow/default.nix b/pkgs/development/python-modules/marshmallow/default.nix
index 242244726e5..20543faeb16 100644
--- a/pkgs/development/python-modules/marshmallow/default.nix
+++ b/pkgs/development/python-modules/marshmallow/default.nix
@@ -4,7 +4,7 @@
 
 buildPythonPackage rec {
   pname = "marshmallow";
-  version = "2.15.3";
+  version = "2.15.4";
 
   meta = {
     homepage = "https://github.com/marshmallow-code/marshmallow";
@@ -17,7 +17,7 @@ buildPythonPackage rec {
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "171f409d48b44786b7df2793cbd7f1a9062f0fe2c14d547da536b5010f671ade";
+    sha256 = "0f3776aa5b5405f6000c9304841abe6d4d708bb08207fc89a5ecd86622ec9e54";
   };
 
   propagatedBuildInputs = [ dateutil simplejson ];
diff --git a/pkgs/development/python-modules/matplotlib/default.nix b/pkgs/development/python-modules/matplotlib/default.nix
index 794124ef3bf..f9aa8cb2ebe 100644
--- a/pkgs/development/python-modules/matplotlib/default.nix
+++ b/pkgs/development/python-modules/matplotlib/default.nix
@@ -21,12 +21,12 @@ assert enableTk -> (tcl != null)
 assert enableQt -> pyqt4 != null;
 
 buildPythonPackage rec {
-  version = "2.2.2";
+  version = "2.2.3";
   pname = "matplotlib";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "4dc7ef528aad21f22be85e95725234c5178c0f938e2228ca76640e5e84d8cde8";
+    sha256 = "7355bf757ecacd5f0ac9dd9523c8e1a1103faadf8d33c22664178e17533f8ce5";
   };
 
   NIX_CFLAGS_COMPILE = stdenv.lib.optionalString stdenv.isDarwin "-I${libcxx}/include/c++/v1";
diff --git a/pkgs/development/python-modules/more-itertools/default.nix b/pkgs/development/python-modules/more-itertools/default.nix
index 6a58a6a8a28..b7131902962 100644
--- a/pkgs/development/python-modules/more-itertools/default.nix
+++ b/pkgs/development/python-modules/more-itertools/default.nix
@@ -3,24 +3,29 @@
 , fetchPypi
 , nose
 , six
+, stdenv
 }:
 
 
 buildPythonPackage rec {
   pname = "more-itertools";
-  version = "4.2.0";
+  version = "4.3.0";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "2b6b9893337bfd9166bee6a62c2b0c9fe7735dcf85948b387ec8cba30e85d8e8";
+    sha256 = "c476b5d3a34e12d40130bc2f935028b5f636df8f372dc2c1c01dc19681b2039e";
   };
 
   checkInputs = [ nose ];
   propagatedBuildInputs = [ six ];
 
+  # iterable = range(10 ** 10)  # Is efficiently reversible
+  # OverflowError: Python int too large to convert to C long
+  doCheck = !stdenv.hostPlatform.is32bit;
+
   meta = {
     homepage = https://more-itertools.readthedocs.org;
     description = "Expansion of the itertools module";
     license = lib.licenses.mit;
   };
-}
\ No newline at end of file
+}
diff --git a/pkgs/development/python-modules/moto/default.nix b/pkgs/development/python-modules/moto/default.nix
index cfb70724210..f9d1fee8973 100644
--- a/pkgs/development/python-modules/moto/default.nix
+++ b/pkgs/development/python-modules/moto/default.nix
@@ -1,14 +1,14 @@
 { buildPythonPackage, fetchPypi, jinja2, werkzeug, flask
 , requests, pytz, backports_tempfile, cookies, jsondiff, botocore, aws-xray-sdk, docker, responses
-, six, boto, httpretty, xmltodict, nose, sure, boto3, freezegun, dateutil, mock, pyaml }:
+, six, boto, httpretty, xmltodict, nose, sure, boto3, freezegun, dateutil, mock, pyaml, python-jose }:
 
 buildPythonPackage rec {
   pname = "moto";
-  version = "1.3.3";
+  version = "1.3.5";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "45d14aca2b06b0083d5e82cfd770ebca0ba77b5070aec6928670240939a78681";
+    sha256 = "52426f2567e51ba73fdc7c7d617236b7e7918dca2421caabe13e5290942b53d8";
   };
 
   postPatch = ''
@@ -42,6 +42,7 @@ buildPythonPackage rec {
     botocore
     docker
     responses
+    python-jose
   ];
 
   checkInputs = [ boto3 nose sure freezegun ];
diff --git a/pkgs/development/python-modules/multipledispatch/default.nix b/pkgs/development/python-modules/multipledispatch/default.nix
index f568e53c573..8b2de6c5af1 100644
--- a/pkgs/development/python-modules/multipledispatch/default.nix
+++ b/pkgs/development/python-modules/multipledispatch/default.nix
@@ -1,20 +1,23 @@
 { lib
 , buildPythonPackage
 , fetchPypi
+, six
 }:
 
 buildPythonPackage rec {
   pname = "multipledispatch";
-  version = "0.5.0";
+  version = "0.6.0";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "9e92d63efad2c9b68562175d9148d8cb32d04bf5557991190e643749bf4ed954";
+    sha256 = "a7ab1451fd0bf9b92cab3edbd7b205622fb767aeefb4fb536c2e3de9e0a38bea";
   };
 
   # No tests in archive
   doCheck = false;
 
+  propagatedBuildInputs = [ six ];
+
   meta = {
     homepage = https://github.com/mrocklin/multipledispatch/;
     description = "A relatively sane approach to multiple dispatch in Python";
diff --git a/pkgs/development/python-modules/mutagen/default.nix b/pkgs/development/python-modules/mutagen/default.nix
index 054d0247600..78271de6f69 100644
--- a/pkgs/development/python-modules/mutagen/default.nix
+++ b/pkgs/development/python-modules/mutagen/default.nix
@@ -10,11 +10,11 @@
 
 buildPythonPackage rec {
   pname = "mutagen";
-  version = "1.41.0";
+  version = "1.41.1";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "dab6038c7f0e17c1b67fb8f56303e8be21e73ac47760f1a8e716856f1bdf5057";
+    sha256 = "2ea9c900a05fa7f5f4c5bd9fc1475d7d576532e13b2f79b694452b997ff67200";
   };
 
   checkInputs = [
diff --git a/pkgs/development/python-modules/natsort/default.nix b/pkgs/development/python-modules/natsort/default.nix
index e952129f15d..561135dda57 100644
--- a/pkgs/development/python-modules/natsort/default.nix
+++ b/pkgs/development/python-modules/natsort/default.nix
@@ -4,8 +4,6 @@
 , fetchPypi
 , hypothesis
 , pytestcache
-, pytestflakes
-, pytestpep8
 , pytest
 , glibcLocales
 , mock ? null
@@ -19,8 +17,6 @@ buildPythonPackage rec {
   checkInputs = [
     hypothesis
     pytestcache
-    pytestflakes
-    pytestpep8
     pytest
     glibcLocales
   ]
@@ -37,7 +33,7 @@ buildPythonPackage rec {
   # testing based on project's tox.ini
   checkPhase = ''
     pytest --doctest-modules natsort
-    pytest --flakes --pep8
+    pytest
   '';
 
   meta = {
diff --git a/pkgs/development/python-modules/ncclient/default.nix b/pkgs/development/python-modules/ncclient/default.nix
index d8a6499d136..9dc7710ff28 100644
--- a/pkgs/development/python-modules/ncclient/default.nix
+++ b/pkgs/development/python-modules/ncclient/default.nix
@@ -11,11 +11,11 @@
 
 buildPythonPackage rec {
   pname = "ncclient";
-  version = "0.6.0";
+  version = "0.6.2";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "da7f7dfb8a60711610139e894b41ebcab3cd7103b78439ad5e9e91c2d3cfa423";
+    sha256 = "6616828f9c5d318906dae22378a78342bbfa5983f1775c1af8bfecc779434c38";
   };
 
   checkInputs = [ nose rednose ];
diff --git a/pkgs/development/python-modules/netcdf4/default.nix b/pkgs/development/python-modules/netcdf4/default.nix
index 0baa323d53c..7e403fb9e56 100644
--- a/pkgs/development/python-modules/netcdf4/default.nix
+++ b/pkgs/development/python-modules/netcdf4/default.nix
@@ -3,13 +3,13 @@
 }:
 buildPythonPackage rec {
   pname = "netCDF4";
-  version = "1.4.0";
+  version = "1.4.1";
 
   disabled = isPyPy;
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "a6c0b46f410f101c09d60b8cc460aafec06732f0130c6cb2730717bcc605b388";
+    sha256 = "d4fc65b98e348c39d082ab6b4b7f6d636b1b4e63bec016e5bca189fee5d46403";
   };
 
   checkInputs = [ pytest ];
diff --git a/pkgs/development/python-modules/nipype/default.nix b/pkgs/development/python-modules/nipype/default.nix
index 3785986ad28..8b0ee06b349 100644
--- a/pkgs/development/python-modules/nipype/default.nix
+++ b/pkgs/development/python-modules/nipype/default.nix
@@ -34,11 +34,11 @@ assert !isPy3k -> configparser != null;
 
 buildPythonPackage rec {
   pname = "nipype";
-  version = "1.1.0";
+  version = "1.1.2";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "2a5ebbc9244a18e3b2d83a9639da09248e92bc0742b81a86550ef1a18c1fccbc";
+    sha256 = "f2fe29bf863cb643bd5c8d2bdeaaf488308c293c9fb9913bc7a9504dc3bf8db6";
   };
 
   # see https://github.com/nipy/nipype/issues/2240
diff --git a/pkgs/development/python-modules/numexpr/default.nix b/pkgs/development/python-modules/numexpr/default.nix
index 09f6c6636c1..6e237b2bd9e 100644
--- a/pkgs/development/python-modules/numexpr/default.nix
+++ b/pkgs/development/python-modules/numexpr/default.nix
@@ -7,11 +7,11 @@
 
 buildPythonPackage rec {
   pname = "numexpr";
-  version = "2.6.6";
+  version = "2.6.8";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "97c1f7fa409439ae933494014cd41d43de84cfe6c98b7f93392f94d54de1b453";
+    sha256 = "ee8bc7201aa2f1962c67d27c326a11eef9df887d7b87b1278a1d4e722bf44375";
   };
 
   propagatedBuildInputs = [ numpy ];
@@ -19,20 +19,15 @@ buildPythonPackage rec {
   # Run the test suite.
   # It requires the build path to be in the python search path.
   checkPhase = ''
+    pushd $out
     ${python}/bin/${python.executable} <<EOF
-    import sysconfig
     import sys
-    import os
-    f = "lib.{platform}-{version[0]}.{version[1]}"
-    lib = f.format(platform=sysconfig.get_platform(),
-                   version=sys.version_info)
-    build = os.path.join(os.getcwd(), 'build', lib)
-    sys.path.insert(0, build)
     import numexpr
     r = numexpr.test()
     if not r.wasSuccessful():
         sys.exit(1)
     EOF
+    popd
   '';
 
   meta = {
diff --git a/pkgs/development/python-modules/numpy/default.nix b/pkgs/development/python-modules/numpy/default.nix
index 5577004465e..af8815dbfb1 100644
--- a/pkgs/development/python-modules/numpy/default.nix
+++ b/pkgs/development/python-modules/numpy/default.nix
@@ -1,17 +1,17 @@
-{ stdenv, lib, fetchPypi, python, buildPythonPackage, isPyPy, gfortran, nose, blas }:
+{ stdenv, lib, fetchPypi, python, buildPythonPackage, isPyPy, gfortran, pytest, blas }:
 
 buildPythonPackage rec {
   pname = "numpy";
-  version = "1.14.5";
+  version = "1.15.1";
 
   src = fetchPypi {
     inherit pname version;
     extension = "zip";
-    sha256 = "a4a433b3a264dbc9aa9c7c241e87c0358a503ea6394f8737df1683c7c9a102ac";
+    sha256 = "7b9e37f194f8bcdca8e9e6af92e2cbad79e360542effc2dd6b98d63955d8d8a3";
   };
 
   disabled = isPyPy;
-  buildInputs = [ gfortran nose blas ];
+  buildInputs = [ gfortran pytest blas ];
 
   patches = lib.optionals (python.hasDistutilsCxxPatch or false) [
     # We patch cpython/distutils to fix https://bugs.python.org/issue1222585
@@ -56,10 +56,6 @@ buildPythonPackage rec {
     runHook postCheck
   '';
 
-  postInstall = ''
-    ln -s $out/bin/f2py* $out/bin/f2py
-  '';
-
   passthru = {
     blas = blas;
   };
diff --git a/pkgs/development/python-modules/oauthenticator/default.nix b/pkgs/development/python-modules/oauthenticator/default.nix
index 362554b9bb8..f35562d7c42 100644
--- a/pkgs/development/python-modules/oauthenticator/default.nix
+++ b/pkgs/development/python-modules/oauthenticator/default.nix
@@ -16,11 +16,11 @@
 
 buildPythonPackage rec {
   pname = "oauthenticator";
-  version = "0.7.3";
+  version = "0.8.0";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "cb0b2564e46db28350693bc3e6457333c4ee21af5066ac743730e3f3173ea7ed";
+    sha256 = "39908f01cda98186c0fedc350b68342d6016ee325615f4c8475c1e64a55d9e4f";
   };
 
   checkPhase = ''
diff --git a/pkgs/development/python-modules/openpyxl/default.nix b/pkgs/development/python-modules/openpyxl/default.nix
index 7b8f4602140..6445201c40b 100644
--- a/pkgs/development/python-modules/openpyxl/default.nix
+++ b/pkgs/development/python-modules/openpyxl/default.nix
@@ -9,11 +9,11 @@
 
 buildPythonPackage rec {
   pname = "openpyxl";
-  version = "2.5.4";
+  version = "2.5.6";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "9239b74faf175dc4276a5fc277655fc53c2f704ded39e680d35e6a39e1913f69";
+    sha256 = "04091e034911a0afc531c3a15e5ae0b1b6a43654dbf63c187f47d20cdfefac1c";
   };
 
   checkInputs = [ pytest ];
diff --git a/pkgs/development/python-modules/pandas/default.nix b/pkgs/development/python-modules/pandas/default.nix
index 9e4ed217b92..02427a52425 100644
--- a/pkgs/development/python-modules/pandas/default.nix
+++ b/pkgs/development/python-modules/pandas/default.nix
@@ -28,11 +28,11 @@ let
 
 in buildPythonPackage rec {
   pname = "pandas";
-  version = "0.23.3";
+  version = "0.23.4";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "9cd3614b4e31a0889388ff1bd19ae857ad52658b33f776065793c293a29cf612";
+    sha256 = "5b24ca47acf69222e82530e89111dd9d14f9b970ab2cd3a1c2c78f0c4fbba4f4";
   };
 
   checkInputs = [ pytest glibcLocales moto ];
@@ -80,6 +80,8 @@ in buildPythonPackage rec {
     "test_oo_optimizable"
     # Disable IO related tests because IO data is no longer distributed
     "io"
+    # KeyError Timestamp
+    "test_to_excel"
   ] ++ optionals isDarwin [
     "test_locale"
     "test_clipboard"
diff --git a/pkgs/development/python-modules/pathlib/default.nix b/pkgs/development/python-modules/pathlib/default.nix
new file mode 100644
index 00000000000..d70178dac85
--- /dev/null
+++ b/pkgs/development/python-modules/pathlib/default.nix
@@ -0,0 +1,28 @@
+{ lib
+, buildPythonPackage
+, fetchPypi
+, python
+, pythonAtLeast
+}:
+
+buildPythonPackage rec {
+  pname = "pathlib";
+  version = "1.0.1";
+  disabled = pythonAtLeast "3.4"; # Was added to std library in Python 3.4
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "17zajiw4mjbkkv6ahp3xf025qglkj0805m9s41c45zryzj6p2h39";
+  };
+
+  checkPhase = ''
+    ${python.interpreter} -m unittest discover
+  '';
+
+  meta = {
+    description = "Object-oriented filesystem paths";
+    homepage = https://pathlib.readthedocs.org/;
+    license = lib.licenses.mit;
+    maintainers = with lib.maintainers; [ costrouc ];
+  };
+}
diff --git a/pkgs/development/python-modules/pathspec/default.nix b/pkgs/development/python-modules/pathspec/default.nix
index 4d812ec3b4f..15ff1b32241 100644
--- a/pkgs/development/python-modules/pathspec/default.nix
+++ b/pkgs/development/python-modules/pathspec/default.nix
@@ -5,12 +5,12 @@
 
 buildPythonPackage rec {
   pname   = "pathspec";
-  version = "0.5.6";
+  version = "0.5.7";
   name    = "${pname}-${version}";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "be664567cf96a718a68b33329862d1e6f6803ef9c48a6e2636265806cfceb29d";
+    sha256 = "69ac7869c9ce308cfe631e29c09f9da60fae02baf31418885bbbb0c75adcd8c5";
   };
 
   meta = {
diff --git a/pkgs/development/python-modules/pbr/default.nix b/pkgs/development/python-modules/pbr/default.nix
index 666df965f87..e1843e4a75d 100644
--- a/pkgs/development/python-modules/pbr/default.nix
+++ b/pkgs/development/python-modules/pbr/default.nix
@@ -2,11 +2,11 @@
 
 buildPythonPackage rec {
   pname = "pbr";
-  version = "4.1.1";
+  version = "4.2.0";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "754e766b4f4bad3aa68cfd532456298da1aa39375da8748392dbae90860d5f18";
+    sha256 = "1b8be50d938c9bb75d0eaf7eda111eec1bf6dc88a62a6412e33bf077457e0f45";
   };
 
   # circular dependencies with fixtures
diff --git a/pkgs/development/python-modules/pendulum/default.nix b/pkgs/development/python-modules/pendulum/default.nix
index 5368a4f878e..e9d482e42ac 100644
--- a/pkgs/development/python-modules/pendulum/default.nix
+++ b/pkgs/development/python-modules/pendulum/default.nix
@@ -3,11 +3,11 @@
 
 buildPythonPackage rec {
   pname = "pendulum";
-  version = "2.0.2";
+  version = "2.0.3";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "544e44d8a92954e5ef4db4fa8b662d3282f2ac7b7c2cbf4227dc193ba78b9e1e";
+    sha256 = "d07962450e808556b3e6209a5830e2bbf8c7747129580c3b5b09e641f72617ab";
   };
 
   propagatedBuildInputs = [ dateutil pytzdata ] ++ lib.optional (pythonOlder "3.5") typing;
diff --git a/pkgs/development/python-modules/persistent/default.nix b/pkgs/development/python-modules/persistent/default.nix
index 4f2e7f3ca84..542a68728af 100644
--- a/pkgs/development/python-modules/persistent/default.nix
+++ b/pkgs/development/python-modules/persistent/default.nix
@@ -5,13 +5,13 @@
 
 buildPythonPackage rec {
   pname = "persistent";
-  version = "4.2.4.2";
+  version = "4.4.2";
 
   propagatedBuildInputs = [ zope_interface ];
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "cf264cd55866c7ffbcbe1328f8d8b28fd042a5dd0c03a03f68c0887df3aa1964";
+    sha256 = "451c756b4f4faa5f06f87d57f5928758bb3a16a586ceaa8773c35367188eddf9";
   };
 
   meta = {
diff --git a/pkgs/development/python-modules/phonenumbers/default.nix b/pkgs/development/python-modules/phonenumbers/default.nix
index 79a5a646ead..a6ca8fae7cb 100644
--- a/pkgs/development/python-modules/phonenumbers/default.nix
+++ b/pkgs/development/python-modules/phonenumbers/default.nix
@@ -2,11 +2,11 @@
 
 buildPythonPackage rec {
   pname = "phonenumbers";
-  version = "8.9.10";
+  version = "8.9.12";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "cbb8194814cc026f476132c38c507adbd459bc8ee99be39f421650ab1b986ed7";
+    sha256 = "39cd0c67a17a9ca4c2851ab8fad5272948d811ccd2a8e52ddcc8d275a802af70";
   };
 
   meta = {
diff --git a/pkgs/development/python-modules/phonopy/default.nix b/pkgs/development/python-modules/phonopy/default.nix
index 57ddeeeb8ec..cf15ccc18fc 100644
--- a/pkgs/development/python-modules/phonopy/default.nix
+++ b/pkgs/development/python-modules/phonopy/default.nix
@@ -2,11 +2,11 @@
 
 buildPythonPackage rec {
   pname = "phonopy";
-  version = "1.13.2.13";
+  version = "1.13.2.107";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "23970ecdf698e743f9204711e8edfbb33c97667f5f88c7bda3322abbc91d0682";
+    sha256 = "72f06728c98b9a7ab3db2d6fa2ae5d029029fbcff4e8fcfbc29f1e2620a0f905";
   };
 
   propagatedBuildInputs = [ numpy pyyaml matplotlib h5py ];
diff --git a/pkgs/development/python-modules/pkgconfig/default.nix b/pkgs/development/python-modules/pkgconfig/default.nix
index b810213cce9..96c0ea56682 100644
--- a/pkgs/development/python-modules/pkgconfig/default.nix
+++ b/pkgs/development/python-modules/pkgconfig/default.nix
@@ -2,11 +2,11 @@
 
 buildPythonPackage rec {
   pname = "pkgconfig";
-  version = "1.3.1";
+  version = "1.4.0";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "107x2wmchlch8saixb488cgjz9n6inl38wi7nxkb942rbaapxiqb";
+    sha256 = "048c3b457da7b6f686b647ab10bf09e2250e4c50acfe6f215398a8b5e6fcdb52";
   };
 
   checkInputs = [ nose ];
diff --git a/pkgs/development/python-modules/plac/default.nix b/pkgs/development/python-modules/plac/default.nix
index c16c8d3f750..d0e7b0d81ee 100644
--- a/pkgs/development/python-modules/plac/default.nix
+++ b/pkgs/development/python-modules/plac/default.nix
@@ -5,11 +5,11 @@
 }:
 buildPythonPackage rec {
   pname = "plac";
-  version = "0.9.6";
+  version = "1.0.0";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "16zqpalx4i1n1hrcvaj8sdixapy2g76fc13bbahz0xc106d72gxs";
+    sha256 = "b03f967f535b3bf5a71b191fa5eb09872a5cfb1e3b377efc4138995e10ba36d7";
   };
 
   checkPhase = ''
diff --git a/pkgs/development/python-modules/plotly/default.nix b/pkgs/development/python-modules/plotly/default.nix
index 6e7147e4e12..30293e9798b 100644
--- a/pkgs/development/python-modules/plotly/default.nix
+++ b/pkgs/development/python-modules/plotly/default.nix
@@ -11,11 +11,11 @@
 
 buildPythonPackage rec {
   pname = "plotly";
-  version = "3.1.0";
+  version = "3.1.1";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "015a5b8ca616d19eb96433dd597c3ccccc80e3afba02a23bd526a017ff4fce05";
+    sha256 = "2e565c8907ea6f9c517423cf5452e4f4b85635bd0dd400aae943339c826d4176";
   };
 
   propagatedBuildInputs = [
diff --git a/pkgs/development/python-modules/pluggy/default.nix b/pkgs/development/python-modules/pluggy/default.nix
index 2a6996c628e..236c0213392 100644
--- a/pkgs/development/python-modules/pluggy/default.nix
+++ b/pkgs/development/python-modules/pluggy/default.nix
@@ -1,15 +1,16 @@
 { buildPythonPackage
 , lib
 , fetchPypi
+, setuptools_scm
 }:
 
 buildPythonPackage rec {
   pname = "pluggy";
-  version = "0.6.0";
+  version = "0.7.1";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "7f8ae7f5bdf75671a718d2daf0a64b7885f74510bcd98b1a0bb420eb9a9d0cff";
+    sha256 = "95eb8364a4708392bae89035f45341871286a333f749c3141c20573d2b3876e1";
   };
 
   checkPhase = ''
@@ -19,6 +20,8 @@ buildPythonPackage rec {
   # To prevent infinite recursion with pytest
   doCheck = false;
 
+  buildInputs = [ setuptools_scm ];
+
   meta = {
     description = "Plugin and hook calling mechanisms for Python";
     homepage = "https://pypi.python.org/pypi/pluggy";
diff --git a/pkgs/development/python-modules/plumbum/default.nix b/pkgs/development/python-modules/plumbum/default.nix
index 2c6eb7e5fbf..13afce05ef7 100644
--- a/pkgs/development/python-modules/plumbum/default.nix
+++ b/pkgs/development/python-modules/plumbum/default.nix
@@ -5,7 +5,7 @@
 
 buildPythonPackage rec {
   pname = "plumbum";
-  version = "1.6.6";
+  version = "1.6.7";
 
   checkInputs = [ pytest ];
 
@@ -14,6 +14,6 @@ buildPythonPackage rec {
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "d179b90a9927f91427a28c1bac2864c61342cb43ef39aa7324c7c9a96bcc23eb";
+    sha256 = "d143f079bfb60b11e9bec09a49695ce2e55ce5ca0246877bdb0818ab7c7fc312";
   };
 }
\ No newline at end of file
diff --git a/pkgs/development/python-modules/plyfile/default.nix b/pkgs/development/python-modules/plyfile/default.nix
index 1ac8afc8cfb..6a7f09a1451 100644
--- a/pkgs/development/python-modules/plyfile/default.nix
+++ b/pkgs/development/python-modules/plyfile/default.nix
@@ -3,11 +3,11 @@
 
 buildPythonPackage rec {
   pname = "plyfile";
-  version = "0.5";
+  version = "0.6";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "1cspvhfy2nw1rfwpvrd69wkz0b6clr4wzqpwpmdk872vk2q89yzi";
+    sha256 = "067e384e3723f28dbbd8e8f976a9712dadf6761b2d62c4c1a90821e3c5310bce";
   };
 
   propagatedBuildInputs = [ numpy ];
diff --git a/pkgs/development/python-modules/prometheus_client/default.nix b/pkgs/development/python-modules/prometheus_client/default.nix
index be014bc0f7e..4529ad95175 100644
--- a/pkgs/development/python-modules/prometheus_client/default.nix
+++ b/pkgs/development/python-modules/prometheus_client/default.nix
@@ -2,11 +2,11 @@
 
 buildPythonPackage rec {
   pname = "prometheus_client";
-  version = "0.3.0";
+  version = "0.3.1";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "69494dc1ac967c0f626c8193e439755c2b95dd4ed22ef31c277601778a50c7ff";
+    sha256 = "17bc24c09431644f7c65d7bce9f4237252308070b6395d6d8e87767afe867e24";
   };
 
   doCheck = false;
diff --git a/pkgs/development/python-modules/psutil/default.nix b/pkgs/development/python-modules/psutil/default.nix
index 84fe2f69554..6e048467313 100644
--- a/pkgs/development/python-modules/psutil/default.nix
+++ b/pkgs/development/python-modules/psutil/default.nix
@@ -6,11 +6,11 @@
 
 buildPythonPackage rec {
   pname = "psutil";
-  version = "5.4.6";
+  version = "5.4.7";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "686e5a35fe4c0acc25f3466c32e716f2d498aaae7b7edc03e2305b682226bcf6";
+    sha256 = "5b6322b167a5ba0c5463b4d30dfd379cd4ce245a1162ebf8fc7ab5c5ffae4f3b";
   };
 
   # No tests in archive
diff --git a/pkgs/development/python-modules/py-cpuinfo/default.nix b/pkgs/development/python-modules/py-cpuinfo/default.nix
new file mode 100644
index 00000000000..37cf601695e
--- /dev/null
+++ b/pkgs/development/python-modules/py-cpuinfo/default.nix
@@ -0,0 +1,23 @@
+{ lib
+, fetchFromGitHub
+, buildPythonPackage
+}:
+
+buildPythonPackage rec {
+  pname = "py-cpuinfo";
+  version = "4.0.0";
+
+  src = fetchFromGitHub {
+     owner = "workhorsy";
+     repo = pname;
+     rev = "v${version}";
+     sha256 = "1pp561lj80jnvr2038nrzhmks2akxsbdqxvfrqa6n340x81981lm";
+  };
+
+  meta = {
+    description = "Get CPU info with pure Python 2 & 3";
+    homepage = https://github.com/workhorsy/py-cpuinfo;
+    license = lib.licenses.mit;
+    maintainers = with lib.maintainers; [ costrouc ];
+  };
+}
diff --git a/pkgs/development/python-modules/py3status/default.nix b/pkgs/development/python-modules/py3status/default.nix
index e47771d5ca0..8a7dcc63f57 100644
--- a/pkgs/development/python-modules/py3status/default.nix
+++ b/pkgs/development/python-modules/py3status/default.nix
@@ -18,10 +18,10 @@
 
 buildPythonPackage rec {
   pname = "py3status";
-  version = "3.11";
+  version = "3.12";
   src = fetchPypi {
     inherit pname version;
-    sha256 = "ba6930427d57b79cf344262494fdcbddbf75f6e37794489d445f2ebb8bc53ec5";
+    sha256 = "c9ef49f72c2d83976d2841ab7e70faee3c77f4d7dbb2d3390ef0f0509473ea9a";
   };
   doCheck = false;
   propagatedBuildInputs = [ pytz requests tzlocal ];
diff --git a/pkgs/development/python-modules/pyaxmlparser/default.nix b/pkgs/development/python-modules/pyaxmlparser/default.nix
index 483ad84eb66..7f9cbf9518e 100644
--- a/pkgs/development/python-modules/pyaxmlparser/default.nix
+++ b/pkgs/development/python-modules/pyaxmlparser/default.nix
@@ -1,12 +1,12 @@
 { buildPythonPackage, stdenv, lxml, click, fetchPypi }:
 
 buildPythonPackage rec {
-  version = "0.3.9";
+  version = "0.3.10";
   pname = "pyaxmlparser";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "af714d8adafcea776dd14cbd6d09f5d6d278f7ba333f540dde3b4c34f5f04784";
+    sha256 = "5c1f569f4dc2232d7f146eb190bc513373ff6555f97ae904740f966f0fb2dd77";
   };
 
   propagatedBuildInputs = [ lxml click ];
diff --git a/pkgs/development/python-modules/pycryptodome/default.nix b/pkgs/development/python-modules/pycryptodome/default.nix
index 27ccc7f4687..5b729182ca8 100644
--- a/pkgs/development/python-modules/pycryptodome/default.nix
+++ b/pkgs/development/python-modules/pycryptodome/default.nix
@@ -1,12 +1,12 @@
 { stdenv, fetchPypi, buildPythonPackage }:
 
 buildPythonPackage rec {
-  version = "3.6.4";
+  version = "3.6.6";
   pname = "pycryptodome";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "9c7790ffd291c81b934fe0ca8155a67235d33f70d4914bbf7467a447d9dbcb09";
+    sha256 = "b3cb4af317d9b84f6df50f0cfa6840ba69556af637a83fd971537823e13d601a";
   };
 
   meta = {
diff --git a/pkgs/development/python-modules/pycryptodomex/default.nix b/pkgs/development/python-modules/pycryptodomex/default.nix
index b5487a24b77..f3f439bc4a5 100644
--- a/pkgs/development/python-modules/pycryptodomex/default.nix
+++ b/pkgs/development/python-modules/pycryptodomex/default.nix
@@ -2,7 +2,7 @@
 
 buildPythonPackage rec {
   pname = "pycryptodomex";
-  version = "3.6.4";
+  version = "3.6.6";
 
   meta = {
     description = "A self-contained cryptographic library for Python";
@@ -12,6 +12,6 @@ buildPythonPackage rec {
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "4daabe7c0404e673b9029aa43761c779b9b4df2cbe11ccd94daded6a0acd8808";
+    sha256 = "d0d448484e161786922b41e112b5d7cf76ef5f0c725ea5107ef866bb14a38b12";
   };
 }
diff --git a/pkgs/development/python-modules/pycuda/default.nix b/pkgs/development/python-modules/pycuda/default.nix
index 2774a363f85..2d1da5339af 100644
--- a/pkgs/development/python-modules/pycuda/default.nix
+++ b/pkgs/development/python-modules/pycuda/default.nix
@@ -22,11 +22,11 @@ let
 in
 buildPythonPackage rec {
   pname = "pycuda";
-  version = "2017.1.1";
+  version = "2018.1";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "0qxmcjax32p1ywicw9sha2rvfbak4kjbx9pq57j3wq4cwf296nkb";
+    sha256 = "7079f7738e83ee79ae26f0827ada29fe55921fec9760201199cc2bfb69446c92";
   };
 
   preConfigure = ''
diff --git a/pkgs/development/python-modules/pygmo/default.nix b/pkgs/development/python-modules/pygmo/default.nix
new file mode 100644
index 00000000000..2500121dc9e
--- /dev/null
+++ b/pkgs/development/python-modules/pygmo/default.nix
@@ -0,0 +1,48 @@
+{ lib
+, fetchFromGitHub
+, buildPythonPackage
+, cmake
+, eigen
+, nlopt
+, ipopt
+, boost
+, pagmo2
+, numpy
+, cloudpickle
+, ipyparallel
+, numba
+}:
+
+buildPythonPackage rec {
+  pname = "pygmo";
+  version = "2.8";
+
+  src = fetchFromGitHub {
+     owner = "esa";
+     repo = "pagmo2";
+     rev = "v${version}";
+     sha256 = "1xwxamcn3fkwr62jn6bkanrwy0cvsksf75hfwx4fvl56awnbz41z";
+  };
+
+  buildInputs = [ cmake eigen nlopt ipopt boost pagmo2 ];
+  propagatedBuildInputs = [ numpy cloudpickle ipyparallel numba ];
+
+  preBuild = ''
+    cp -v -r $src/* .
+    cmake -DCMAKE_INSTALL_PREFIX=$out -DPAGMO_BUILD_TESTS=no -DCMAKE_SYSTEM_NAME=Linux -DPagmo_DIR=${pagmo2} -DPAGMO_BUILD_PYGMO=yes -DPAGMO_BUILD_PAGMO=no -DPAGMO_WITH_EIGEN3=yes -DPAGMO_WITH_NLOPT=yes -DNLOPT_LIBRARY=${nlopt}/lib/libnlopt_cxx.so -DPAGMO_WITH_IPOPT=yes -DIPOPT=${ipopt}
+
+    make install
+    mv $out/lib/python*/site-packages/pygmo wheel
+    cd wheel
+  '';
+
+  # dont do tests
+  doCheck = false;
+
+  meta = {
+    description = "Parallel optimisation for Python";
+    homepage = https://esa.github.io/pagmo2/;
+    license = lib.licenses.gpl3Plus;
+    maintainers = with lib.maintainers; [ costrouc ];
+  };
+}
diff --git a/pkgs/development/python-modules/pyhomematic/default.nix b/pkgs/development/python-modules/pyhomematic/default.nix
index 4ec77ed96c1..cd10edd2b64 100644
--- a/pkgs/development/python-modules/pyhomematic/default.nix
+++ b/pkgs/development/python-modules/pyhomematic/default.nix
@@ -2,13 +2,13 @@
 
 buildPythonPackage rec {
   pname = "pyhomematic";
-  version = "0.1.46";
+  version = "0.1.47";
 
   disabled = !isPy3k;
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "0a0ba8de05fc6d60bbb0beec7e808fb231abcb566c3bc17de532f72b18fe2837";
+    sha256 = "bdac91dc6810b3d9f53d26daf6e6f26480c556fc3b43890e376aa23c17afd60b";
   };
 
   # PyPI tarball does not include tests/ directory
diff --git a/pkgs/development/python-modules/pylast/default.nix b/pkgs/development/python-modules/pylast/default.nix
index 89ae2f37d10..64479a7b5af 100644
--- a/pkgs/development/python-modules/pylast/default.nix
+++ b/pkgs/development/python-modules/pylast/default.nix
@@ -2,11 +2,11 @@
 
 buildPythonPackage rec {
   pname = "pylast";
-  version = "2.3.0";
+  version = "2.4.0";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "f1e8615bac27386712ab74338e6dbd01ff7adbf6648a3debf921cef6bad80014";
+    sha256 = "8e883f13b70c3879fc821bbee1accf27ea4e68898f4462cbbe358f615adcbbfb";
   };
 
   propagatedBuildInputs = [ certifi six ];
diff --git a/pkgs/development/python-modules/pylint/default.nix b/pkgs/development/python-modules/pylint/default.nix
index 0156e92738a..c9a44548c14 100644
--- a/pkgs/development/python-modules/pylint/default.nix
+++ b/pkgs/development/python-modules/pylint/default.nix
@@ -3,13 +3,13 @@
 
 buildPythonPackage rec {
   pname = "pylint";
-  version = "2.0.1";
+  version = "2.1.1";
 
   disabled = pythonOlder "3.4";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "2c90a24bee8fae22ac98061c896e61f45c5b73c2e0511a4bf53f99ba56e90434";
+    sha256 = "31142f764d2a7cd41df5196f9933b12b7ee55e73ef12204b648ad7e556c119fb";
   };
 
   checkInputs = [ pytest pytestrunner pytest_xdist pyenchant ];
diff --git a/pkgs/development/python-modules/pylti/default.nix b/pkgs/development/python-modules/pylti/default.nix
index 600d6406405..32cef1e5da8 100644
--- a/pkgs/development/python-modules/pylti/default.nix
+++ b/pkgs/development/python-modules/pylti/default.nix
@@ -22,7 +22,7 @@
 
 buildPythonPackage rec {
   pname = "PyLTI";
-  version = "0.6.0";
+  version = "0.7.0";
 
   disabled = !isPy27;
 
@@ -39,7 +39,7 @@ buildPythonPackage rec {
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "b3203c5d0d8a527c092518d82d312757c036055ff628023985ab615ef471e602";
+    sha256 = "80938a235b1ab390f6889a95237d087ea7adde5cc50fcae9c80c49898e8ee78e";
   };
 
   meta = {
diff --git a/pkgs/development/python-modules/pymatgen-lammps/default.nix b/pkgs/development/python-modules/pymatgen-lammps/default.nix
new file mode 100644
index 00000000000..dbe9107c7c8
--- /dev/null
+++ b/pkgs/development/python-modules/pymatgen-lammps/default.nix
@@ -0,0 +1,31 @@
+{ lib
+, fetchurl
+, buildPythonPackage
+, pymatgen
+, lammps
+, pytestrunner
+, pytest
+, isPy3k
+}:
+
+buildPythonPackage rec {
+  pname = "pymatgen-lammps";
+  version = "0.4.5";
+  disabled = (!isPy3k);
+
+  src = fetchurl {
+     url = "https://gitlab.com/costrouc/${pname}/-/archive/v${version}/${pname}-v${version}.tar.gz";
+     sha256 = "0shldl8is3195jmji7dr3zsh1bzxlahaqrmpr28niks7nnfj80fx";
+  };
+
+  buildInputs = [ pytestrunner ];
+  checkInputs = [ pytest ];
+  propagatedBuildInputs = [ pymatgen ];
+
+  meta = {
+    description = "A LAMMPS wrapper using pymatgen";
+    homepage = https://gitlab.com/costrouc/pymatgen-lammps;
+    license = lib.licenses.mit;
+    maintainers = with lib.maintainers; [ costrouc ];
+  };
+}
diff --git a/pkgs/development/python-modules/pymatgen/default.nix b/pkgs/development/python-modules/pymatgen/default.nix
index 874f7bfa308..d810a5d6b4d 100644
--- a/pkgs/development/python-modules/pymatgen/default.nix
+++ b/pkgs/development/python-modules/pymatgen/default.nix
@@ -2,11 +2,11 @@
 
 buildPythonPackage rec {
   pname = "pymatgen";
-  version = "2018.6.27";
+  version = "2018.8.10";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "8078af7fda4f9a07f1e389ffe08de3511213acdf9fb2ed9f9ffe89b9b12b8568";
+    sha256 = "9bb3b170ca8654c956fa2efdd31107570c0610f7585d90e4a541eb99cee41603";
   };
 
   nativeBuildInputs = [ glibcLocales ];
diff --git a/pkgs/development/python-modules/pyodbc/default.nix b/pkgs/development/python-modules/pyodbc/default.nix
index ae1133fc0be..b28c1a87647 100644
--- a/pkgs/development/python-modules/pyodbc/default.nix
+++ b/pkgs/development/python-modules/pyodbc/default.nix
@@ -2,12 +2,12 @@
 
 buildPythonPackage rec {
   pname = "pyodbc";
-  version = "4.0.23";
+  version = "4.0.24";
   disabled = isPyPy;  # use pypypdbc instead
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "bb33d032c1f25781db64e2e4fecf77047fab2ddde42a6cd9496e3c66fb8e9f66";
+    sha256 = "4326abb737dec36156998d52324921673d30f575e1e0998f0c5edd7de20e61d4";
   };
 
   buildInputs = [ libiodbc ];
diff --git a/pkgs/development/python-modules/pyowm/default.nix b/pkgs/development/python-modules/pyowm/default.nix
index 55f96416efd..58a8dee155a 100644
--- a/pkgs/development/python-modules/pyowm/default.nix
+++ b/pkgs/development/python-modules/pyowm/default.nix
@@ -2,11 +2,11 @@
 
 buildPythonPackage rec {
   pname = "pyowm";
-  version = "2.8.0";
+  version = "2.9.0";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "0y2r322pcamabar70513pbyiq26x33l1aq9cim6k30lk9p4aq310";
+    sha256 = "ed175873823a2fedb48e453505c974ca39f3f75006ef1af54fdbcf72e6796849";
   };
 
   propagatedBuildInputs = [ requests ];
diff --git a/pkgs/development/python-modules/pyphen/default.nix b/pkgs/development/python-modules/pyphen/default.nix
index 4cc7f1493f8..7a182b6be4a 100644
--- a/pkgs/development/python-modules/pyphen/default.nix
+++ b/pkgs/development/python-modules/pyphen/default.nix
@@ -2,11 +2,11 @@
 
 buildPythonPackage rec {
   pname = "Pyphen";
-  version = "0.9.4";
+  version = "0.9.5";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "1mqb5jrigxipxzp1d8nbwkq0cfjw77pnn6hc4mp1yd2mn059mymb";
+    sha256 = "3b633a50873156d777e1f1075ba4d8e96a6ad0a3ca42aa3ea9a6259f93f18921";
   };
 
   meta = with stdenv.lib; {
diff --git a/pkgs/development/python-modules/pytest-asyncio/default.nix b/pkgs/development/python-modules/pytest-asyncio/default.nix
index e1ff0998396..6b4ce6f6123 100644
--- a/pkgs/development/python-modules/pytest-asyncio/default.nix
+++ b/pkgs/development/python-modules/pytest-asyncio/default.nix
@@ -1,13 +1,13 @@
 { stdenv, buildPythonPackage, fetchPypi, pytest, isPy3k }:
 buildPythonPackage rec {
   pname = "pytest-asyncio";
-  version = "0.8.0";
+  version = "0.9.0";
 
   disabled = !isPy3k;
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "f32804bb58a66e13a3eda11f8942a71b1b6a30466b0d2ffe9214787aab0e172e";
+    sha256 = "fbd92c067c16111174a1286bfb253660f1e564e5146b39eeed1133315cf2c2cf";
   };
 
   buildInputs = [ pytest ];
@@ -15,6 +15,11 @@ buildPythonPackage rec {
   # No tests in archive
   doCheck = false;
 
+  # LICENSE file is not distributed. https://github.com/pytest-dev/pytest-asyncio/issues/92
+  postPatch = ''
+    substituteInPlace setup.cfg --replace "license_file = LICENSE" ""
+  '';
+
   meta = with stdenv.lib; {
     description = "library for testing asyncio code with pytest";
     license = licenses.asl20;
diff --git a/pkgs/development/python-modules/pytest-benchmark/default.nix b/pkgs/development/python-modules/pytest-benchmark/default.nix
new file mode 100644
index 00000000000..0f3475f715d
--- /dev/null
+++ b/pkgs/development/python-modules/pytest-benchmark/default.nix
@@ -0,0 +1,31 @@
+{ lib
+, buildPythonPackage
+, fetchFromGitHub
+, pytestrunner
+, pytest
+, py-cpuinfo
+, pythonOlder
+, pathlib
+, statistics
+}:
+
+buildPythonPackage rec {
+  pname = "pytest-benchmark";
+  version = "3.1.1";
+
+  src = fetchFromGitHub {
+    owner = "ionelmc";
+    repo = pname;
+    rev = "v${version}";
+    sha256 = "1ch079dlc6c9ag74dh4dg6plkmh0h8kn78ari3fgadc75bald71m";
+  };
+
+  propagatedBuildInputs = [ pytest py-cpuinfo ] ++ lib.optional (pythonOlder "3.4") [ pathlib statistics ];
+
+  meta = {
+    description = "Py.test fixture for benchmarking code";
+    homepage = https://github.com/ionelmc/pytest-benchmark;
+    license = lib.licenses.bsd2;
+    maintainers = with lib.maintainers; [ costrouc ];
+  };
+}
diff --git a/pkgs/development/python-modules/pytest-flakes/default.nix b/pkgs/development/python-modules/pytest-flakes/default.nix
index c8ae9882a1e..f8823b966da 100644
--- a/pkgs/development/python-modules/pytest-flakes/default.nix
+++ b/pkgs/development/python-modules/pytest-flakes/default.nix
@@ -3,11 +3,11 @@
 
 buildPythonPackage rec {
   pname = "pytest-flakes";
-  version = "3.0.2";
+  version = "4.0.0";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "763ec290b89e2dc8f25f49d71cb9b869b8df843697b730233f61c78f847f2e57";
+    sha256 = "341964bf5760ebbdde9619f68a17d5632c674c3f6903ef66daa0a4f540b3d143";
   };
 
   buildInputs = [ pytestpep8 pytest ];
diff --git a/pkgs/development/python-modules/pytest-timeout/default.nix b/pkgs/development/python-modules/pytest-timeout/default.nix
index 012226de053..8c697b8b2ec 100644
--- a/pkgs/development/python-modules/pytest-timeout/default.nix
+++ b/pkgs/development/python-modules/pytest-timeout/default.nix
@@ -7,11 +7,11 @@
 
 buildPythonPackage rec {
   pname = "pytest-timeout";
-  version = "1.3.1";
+  version = "1.3.2";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "4b261bec5782b603c98b4bb803484bc96bf1cdcb5480dae0999d21c7e0423a23";
+    sha256 = "1117fc0536e1638862917efbdc0895e6b62fa61e6cf4f39bb655686af7af9627";
   };
   buildInputs = [ pytest ];
   checkInputs = [ pytest pexpect ];
diff --git a/pkgs/development/python-modules/pytest-xdist/default.nix b/pkgs/development/python-modules/pytest-xdist/default.nix
index 2e88a765417..46d505b3801 100644
--- a/pkgs/development/python-modules/pytest-xdist/default.nix
+++ b/pkgs/development/python-modules/pytest-xdist/default.nix
@@ -2,11 +2,11 @@
 
 buildPythonPackage rec {
   pname = "pytest-xdist";
-  version = "1.22.3";
+  version = "1.23.0";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "48868d1f461122ac8c5fb60487b6da03c0d73dcb06a9d79e06c4eab8ef62a5c3";
+    sha256 = "28e25e79698b2662b648319d3971c0f9ae0e6500f88258ccb9b153c31110ba9b";
   };
 
   nativeBuildInputs = [ setuptools_scm ];
diff --git a/pkgs/development/python-modules/pytest/default.nix b/pkgs/development/python-modules/pytest/default.nix
index 0e3f89fa152..3770f62f1a5 100644
--- a/pkgs/development/python-modules/pytest/default.nix
+++ b/pkgs/development/python-modules/pytest/default.nix
@@ -1,9 +1,9 @@
 { stdenv, buildPythonPackage, fetchPypi, attrs, hypothesis, py
 , setuptools_scm, setuptools, six, pluggy, funcsigs, isPy3k, more-itertools
-, atomicwrites, mock, writeText
+, atomicwrites, mock, writeText, pathlib2
 }:
 buildPythonPackage rec {
-  version = "3.6.3";
+  version = "3.7.4";
   pname = "pytest";
 
   preCheck = ''
@@ -13,13 +13,13 @@ buildPythonPackage rec {
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "0453c8676c2bee6feb0434748b068d5510273a916295fd61d306c4f22fbfd752";
+    sha256 = "2d7c49e931316cc7d1638a3e5f54f5d7b4e5225972b3c9838f3584788d27f349";
   };
 
   checkInputs = [ hypothesis mock ];
   buildInputs = [ setuptools_scm ];
   propagatedBuildInputs = [ attrs py setuptools six pluggy more-itertools atomicwrites]
-    ++ (stdenv.lib.optional (!isPy3k) funcsigs);
+    ++ stdenv.lib.optionals (!isPy3k) [ funcsigs pathlib2 ];
 
   checkPhase = ''
     runHook preCheck
diff --git a/pkgs/development/python-modules/pytestrunner/default.nix b/pkgs/development/python-modules/pytestrunner/default.nix
index 71b1260a540..4d9b9b76157 100644
--- a/pkgs/development/python-modules/pytestrunner/default.nix
+++ b/pkgs/development/python-modules/pytestrunner/default.nix
@@ -11,6 +11,17 @@ buildPythonPackage rec {
 
   buildInputs = [ setuptools_scm pytest ];
 
+  postPatch = ''
+    rm pytest.ini
+  '';
+
+  checkPhase = ''
+    py.test tests
+  '';
+
+  # Fixture not found
+  doCheck = false;
+
   meta = with stdenv.lib; {
     description = "Invoke py.test as distutils command with dependency resolution";
     homepage = https://bitbucket.org/pytest-dev/pytest-runner;
diff --git a/pkgs/development/python-modules/python-ctags3/default.nix b/pkgs/development/python-modules/python-ctags3/default.nix
index ba29154df3a..c37abf7b55f 100644
--- a/pkgs/development/python-modules/python-ctags3/default.nix
+++ b/pkgs/development/python-modules/python-ctags3/default.nix
@@ -2,11 +2,11 @@
 
 buildPythonPackage rec {
   pname = "python-ctags3";
-  version = "1.2.4";
+  version = "1.3.0";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "62e1d48a8cd88756767f3f5e3f1b1a81bc84deeb736f0c9480a5b5d066f63c3e";
+    sha256 = "69029185ec70db4180be2b58e9a7245700c7ddcdc9049bf0641448f439112176";
   };
 
   meta = with lib; {
diff --git a/pkgs/development/python-modules/python-daemon/default.nix b/pkgs/development/python-modules/python-daemon/default.nix
index c44af185a10..76544adaf0b 100644
--- a/pkgs/development/python-modules/python-daemon/default.nix
+++ b/pkgs/development/python-modules/python-daemon/default.nix
@@ -2,11 +2,11 @@
 
 buildPythonPackage rec {
   pname = "python-daemon";
-  version = "2.1.2";
+  version = "2.2.0";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "261c859be5c12ae7d4286dc6951e87e9e1a70a882a8b41fd926efc1ec4214f73";
+    sha256 = "aca149ebf7e73f10cd554b2df5c95295d49add8666348eff6195053ec307728c";
   };
 
   # A test fail within chroot builds.
diff --git a/pkgs/development/python-modules/python-docx/default.nix b/pkgs/development/python-modules/python-docx/default.nix
index 11ade481df5..1a85c5256d7 100644
--- a/pkgs/development/python-modules/python-docx/default.nix
+++ b/pkgs/development/python-modules/python-docx/default.nix
@@ -10,11 +10,11 @@
 
 buildPythonPackage rec {
   pname = "python-docx";
-  version = "0.8.6";
+  version = "0.8.7";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "117i84s6fcdsrfckbvznnqgqwhnf1x0523ps16cki8sg9byydv2m";
+    sha256 = "ba9f2a7ca391b78ab385d796b38af3f21bab23c727fc8e0c5e630448d1a11fe3";
   };
 
   checkInputs = [ behave mock pyparsing pytest ];
diff --git a/pkgs/development/python-modules/python-jose/default.nix b/pkgs/development/python-modules/python-jose/default.nix
index cb99e5fa273..68b46743d35 100644
--- a/pkgs/development/python-modules/python-jose/default.nix
+++ b/pkgs/development/python-modules/python-jose/default.nix
@@ -1,29 +1,30 @@
 { stdenv, buildPythonPackage, fetchFromGitHub
-, six, ecdsa, rsa, future, pytest, cryptography, pycryptodome
+, future, six, ecdsa, pycryptodome, pytest, cryptography
 }:
 
 buildPythonPackage rec {
   pname = "python-jose";
-  version = "3.0.0";
+  version = "2.0.2";
 
   # no tests in PyPI tarball
   src = fetchFromGitHub {
     owner = "mpdavis";
     repo = "python-jose";
-    rev = version;
-    sha256 = "1dq8v87abqxv07wi403ywjk9jg1da125fviycqzki48cjxx0dhwj";
+    # 2.0.2 not tagged on GitHub
+    # see https://github.com/mpdavis/python-jose/issues/86
+    rev = "28cc6719eceb89129eed59c25f7bdac015665bdd";
+    sha256 = "03wkq2rszy0rzy5gygsh4s7i6ls8zflgbcvxnflvmh7nis7002fp";
   };
 
   checkInputs = [
     pytest
-    # optional dependencies, but needed in tests
-    cryptography pycryptodome
+    cryptography # optional dependency, but needed in tests
   ];
   checkPhase = ''
     py.test
   '';
 
-  propagatedBuildInputs = [ six ecdsa rsa future ];
+  propagatedBuildInputs = [ future six ecdsa pycryptodome ];
 
   meta = with stdenv.lib; {
     homepage = https://github.com/mpdavis/python-jose;
diff --git a/pkgs/development/python-modules/python_openzwave/default.nix b/pkgs/development/python-modules/python_openzwave/default.nix
index d29365c86ba..e04915a503d 100644
--- a/pkgs/development/python-modules/python_openzwave/default.nix
+++ b/pkgs/development/python-modules/python_openzwave/default.nix
@@ -5,13 +5,13 @@
 
 buildPythonPackage rec {
   pname = "python_openzwave";
-  version = "0.4.7";
+  version = "0.4.9";
 
   disabled = !isPy3k;
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "b28a3abefc04d1d04dd68ee5a695b091e96ba7ab9a9eaa67db43dd55b61a4664";
+    sha256 = "97ddd104f52e3a4d7115c3de5d2136631d1f66627fc9b45d56956c3f2b6e0cdb";
     extension = "zip";
   };
 
diff --git a/pkgs/development/python-modules/pyunifi/default.nix b/pkgs/development/python-modules/pyunifi/default.nix
index 31ec613df4c..e0bc32746e3 100644
--- a/pkgs/development/python-modules/pyunifi/default.nix
+++ b/pkgs/development/python-modules/pyunifi/default.nix
@@ -3,11 +3,11 @@
 
 buildPythonPackage rec {
   pname = "pyunifi";
-  version = "2.13";
+  version = "2.14";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "1dhbfzv5a29v763m0b9wsc4pvkdr979w7g4rz7ak8hsi4sx6b9dq";
+    sha256 = "9439ffc992ce381a39d64b5e3f4460e53872faa9cca60dcf5cee94fc0eba7fca";
   };
 
   propagatedBuildInputs = [ requests ];
diff --git a/pkgs/development/python-modules/pyzmq/default.nix b/pkgs/development/python-modules/pyzmq/default.nix
index 26c453e3a09..31b08d0a9e0 100644
--- a/pkgs/development/python-modules/pyzmq/default.nix
+++ b/pkgs/development/python-modules/pyzmq/default.nix
@@ -9,11 +9,11 @@
 
 buildPythonPackage rec {
   pname = "pyzmq";
-  version = "17.1.0";
+  version = "17.1.2";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "2199f753a230e26aec5238b0518b036780708a4c887d4944519681a920b9dee4";
+    sha256 = "a72b82ac1910f2cf61a49139f4974f994984475f771b0faa730839607eeedddf";
   };
 
   checkInputs = [  pytest tornado ];
diff --git a/pkgs/development/python-modules/qtconsole/default.nix b/pkgs/development/python-modules/qtconsole/default.nix
index 5b35acc0404..67b9a07a36d 100644
--- a/pkgs/development/python-modules/qtconsole/default.nix
+++ b/pkgs/development/python-modules/qtconsole/default.nix
@@ -14,11 +14,11 @@
 
 buildPythonPackage rec {
   pname = "qtconsole";
-  version = "4.3.1";
+  version = "4.4.1";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "eff8c2faeda567a0bef5781f419a64e9977988db101652b312b9d74ec0a5109c";
+    sha256 = "7870b19e6a6b0ab3acc09ee65463c0ca7568b3a01a6902d7c4e1ed2c4fc4e176";
   };
 
   buildInputs = [ nose ] ++ lib.optionals isPy27 [mock];
diff --git a/pkgs/development/python-modules/regex/default.nix b/pkgs/development/python-modules/regex/default.nix
index f3e6d1f5e0a..57d8ca4a263 100644
--- a/pkgs/development/python-modules/regex/default.nix
+++ b/pkgs/development/python-modules/regex/default.nix
@@ -7,11 +7,11 @@
 
 buildPythonPackage rec {
   pname = "regex";
-  version = "2018.07.11";
+  version = "2018.08.29";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "9308dbce8e5ff4ee06b172a777f6c7f650a5835a5ad41a6080eb501639c27a2f";
+    sha256 = "b73cea07117dca888b0c3671770b501bef19aac9c45c8ffdb5bea2cca2377b0a";
   };
 
   postCheck = ''
diff --git a/pkgs/development/python-modules/reikna/default.nix b/pkgs/development/python-modules/reikna/default.nix
index 14e8f9f74ce..760ca0056ff 100644
--- a/pkgs/development/python-modules/reikna/default.nix
+++ b/pkgs/development/python-modules/reikna/default.nix
@@ -13,11 +13,11 @@
 
 buildPythonPackage rec {
   pname = "reikna";
-  version = "0.7.0";
+  version = "0.7.1";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "e27af9a202b8cdedd07793abbd3282806ec724aba091a27c76d7ba8284cfd8ba";
+    sha256 = "0afc5d502cc9ba0dadd88c15d72e2fdaa09fee31faaae5064889732de7940953";
   };
 
   checkInputs = [ sphinx pytestcov pytest ];
diff --git a/pkgs/development/python-modules/reportlab/default.nix b/pkgs/development/python-modules/reportlab/default.nix
index 298c3c79e38..e2f2a7814aa 100644
--- a/pkgs/development/python-modules/reportlab/default.nix
+++ b/pkgs/development/python-modules/reportlab/default.nix
@@ -11,11 +11,11 @@ let
   ft = freetype.overrideAttrs (oldArgs: { dontDisableStatic = true; });
 in buildPythonPackage rec {
   pname = "reportlab";
-  version = "3.5.2";
+  version = "3.5.6";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "08986267eaf25d62c3802512f0a97dc3426d0c82f52c8beb576689582eb85b7f";
+    sha256 = "3836a49e7ea7bce458f437cbc094633c7fd4ac027180565875c18ecc726f261e";
   };
 
   checkInputs = [ glibcLocales ];
diff --git a/pkgs/development/python-modules/rlp/default.nix b/pkgs/development/python-modules/rlp/default.nix
index 381a784d24a..77ada95b301 100644
--- a/pkgs/development/python-modules/rlp/default.nix
+++ b/pkgs/development/python-modules/rlp/default.nix
@@ -2,11 +2,11 @@
 
 buildPythonPackage rec {
   pname = "rlp";
-  version = "1.0.1";
+  version = "1.0.2";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "492c11b18e89af42f98e96bca7671ffee4ad4cf5e69ea23b4d2221157d81b512";
+    sha256 = "040fb5172fa23d27953a886c40cac989fc031d0629db934b5a9edcd2fb28df1e";
   };
 
   checkInputs = [ pytest ];
diff --git a/pkgs/development/python-modules/rope/default.nix b/pkgs/development/python-modules/rope/default.nix
index db08ad2a5c0..e5164f27f56 100644
--- a/pkgs/development/python-modules/rope/default.nix
+++ b/pkgs/development/python-modules/rope/default.nix
@@ -2,11 +2,11 @@
 
 buildPythonPackage rec {
   pname = "rope";
-  version = "0.10.7";
+  version = "0.11.0";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "1lc01pjn0yr6yqcpbf6kk170zg8zhnyzj8kqlsch1mag0g9dz7m0";
+    sha256 = "a108c445e1cd897fe19272ab7877d172e7faf3d4148c80e7d20faba42ea8f7b2";
   };
 
   meta = with stdenv.lib; {
diff --git a/pkgs/development/python-modules/s3fs/default.nix b/pkgs/development/python-modules/s3fs/default.nix
index 0053b125bcb..7a9454734d9 100644
--- a/pkgs/development/python-modules/s3fs/default.nix
+++ b/pkgs/development/python-modules/s3fs/default.nix
@@ -2,11 +2,11 @@
 
 buildPythonPackage rec {
   pname = "s3fs";
-  version = "0.1.5";
+  version = "0.1.6";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "4fbab74d72ceeb1a6f249165bde7b1d1c4dd758390339f52c84f0832bc5117a7";
+    sha256 = "38a3dda6800a5dc6ed697bff8e9a47d84f5c28d186dc25d2ff2f91b445f0dae5";
   };
 
   buildInputs = [ docutils ];
diff --git a/pkgs/development/python-modules/sarge/default.nix b/pkgs/development/python-modules/sarge/default.nix
index cf9e175490d..b2eb0668de6 100644
--- a/pkgs/development/python-modules/sarge/default.nix
+++ b/pkgs/development/python-modules/sarge/default.nix
@@ -9,6 +9,9 @@ buildPythonPackage rec {
     sha256 = "da8cc90883f8e5ab4af0d746438f608662f5f2a35da2e858517927edefa134b0";
   };
 
+  # No tests in PyPI tarball
+  doCheck = false;
+
   meta = with lib; {
     homepage = http://sarge.readthedocs.org/;
     description = "A wrapper for subprocess which provides command pipeline functionality";
diff --git a/pkgs/development/python-modules/scipy/default.nix b/pkgs/development/python-modules/scipy/default.nix
index 41878b19d08..140e8cc80b4 100644
--- a/pkgs/development/python-modules/scipy/default.nix
+++ b/pkgs/development/python-modules/scipy/default.nix
@@ -1,4 +1,4 @@
-{lib, fetchPypi, python, buildPythonPackage, gfortran, nose, pytest, numpy}:
+{lib, fetchPypi, python, buildPythonPackage, gfortran, nose, pytest, numpy, fetchpatch}:
 
 buildPythonPackage rec {
   pname = "scipy";
@@ -18,6 +18,10 @@ buildPythonPackage rec {
     rm scipy/linalg/tests/test_lapack.py
   '';
 
+  # INTERNALERROR, solved with https://github.com/scipy/scipy/pull/8871
+  # however, it does not apply cleanly.
+  doCheck = false;
+
   preConfigure = ''
     sed -i '0,/from numpy.distutils.core/s//import setuptools;from numpy.distutils.core/' setup.py
     export NPY_NUM_BUILD_JOBS=$NIX_BUILD_CORES
diff --git a/pkgs/development/python-modules/setuptools/default.nix b/pkgs/development/python-modules/setuptools/default.nix
index b10cdfae5c7..b61af72909f 100644
--- a/pkgs/development/python-modules/setuptools/default.nix
+++ b/pkgs/development/python-modules/setuptools/default.nix
@@ -8,13 +8,13 @@
 # Should use buildPythonPackage here somehow
 stdenv.mkDerivation rec {
   pname = "setuptools";
-  version = "40.0.0";
+  version = "40.2.0";
   name = "${python.libPrefix}-${pname}-${version}";
 
   src = fetchPypi {
     inherit pname version;
     extension = "zip";
-    sha256 = "012adb8e25fbfd64c652e99e7bab58799a3aaf05d39ab38561f69190a909015f";
+    sha256 = "47881d54ede4da9c15273bac65f9340f8929d4f0213193fa7894be384f2dcfa6";
   };
 
   nativeBuildInputs = [ unzip wrapPython ];
diff --git a/pkgs/development/python-modules/setuptools_scm/default.nix b/pkgs/development/python-modules/setuptools_scm/default.nix
index 1420428e973..f6e0daea5ad 100644
--- a/pkgs/development/python-modules/setuptools_scm/default.nix
+++ b/pkgs/development/python-modules/setuptools_scm/default.nix
@@ -1,11 +1,11 @@
 { stdenv, buildPythonPackage, fetchPypi, pip }:
 buildPythonPackage rec {
   pname = "setuptools_scm";
-  version = "2.1.0";
+  version = "3.1.0";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "a767141fecdab1c0b3c8e4c788ac912d7c94a0d6c452d40777ba84f918316379";
+    sha256 = "1191f2a136b5e86f7ca8ab00a97ef7aef997131f1f6d4971be69a1ef387d8b40";
   };
 
   buildInputs = [ pip ];
diff --git a/pkgs/development/python-modules/simpleeval/default.nix b/pkgs/development/python-modules/simpleeval/default.nix
index b3377e75f67..831cfede950 100644
--- a/pkgs/development/python-modules/simpleeval/default.nix
+++ b/pkgs/development/python-modules/simpleeval/default.nix
@@ -2,10 +2,10 @@
 
 buildPythonPackage rec {
   pname = "simpleeval";
-  version = "0.9.5";
+  version = "0.9.6";
   src = fetchPypi {
     inherit pname version;
-    sha256 = "0sda13bqg9l4j17iczmfanxbzsg6fm9aw8i3crzsjfxx51rwj1i3";
+    sha256 = "848fdb9ee5f30cf93b9f0d840db6e7562633d20abf7d67c2382a0a2162a79410";
   };
   meta = {
     homepage = https://github.com/danthedeckie/simpleeval;
diff --git a/pkgs/development/python-modules/snakeviz/default.nix b/pkgs/development/python-modules/snakeviz/default.nix
index 9a3afc3fb4b..2b0ff6e443a 100644
--- a/pkgs/development/python-modules/snakeviz/default.nix
+++ b/pkgs/development/python-modules/snakeviz/default.nix
@@ -2,11 +2,11 @@
 
 buildPythonPackage rec {
   pname = "snakeviz";
-  version = "0.4.1";
+  version = "1.0.0";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "18vsaw1wmf903fg21zkk6a9b49gj47g52jm5h52g4iygngjhpx79";
+    sha256 = "5fe23667708a4ed04047abfbf209675a8488ea6ea8c038d7de06d8a083fb3531";
   };
 
   # Upstream doesn't run tests from setup.py
diff --git a/pkgs/development/python-modules/sockjs-tornado/default.nix b/pkgs/development/python-modules/sockjs-tornado/default.nix
index b8b67f708e6..32ac94da761 100644
--- a/pkgs/development/python-modules/sockjs-tornado/default.nix
+++ b/pkgs/development/python-modules/sockjs-tornado/default.nix
@@ -2,11 +2,11 @@
 
 buildPythonPackage rec {
   pname = "sockjs-tornado";
-  version = "1.0.3";
+  version = "1.0.5";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "16cff40nniqsyvda1pb2j3b4zwmrw7y2g1vqq78lp20xpmhnwwkd";
+    sha256 = "4c4bcf33c8a238bbab37d01da769bcf89e74ef6019bfa76ddbcb4d682d47187e";
   };
 
   propagatedBuildInputs = [ tornado ];
diff --git a/pkgs/development/python-modules/soco/default.nix b/pkgs/development/python-modules/soco/default.nix
index 152a61bbf1d..d039756eb81 100644
--- a/pkgs/development/python-modules/soco/default.nix
+++ b/pkgs/development/python-modules/soco/default.nix
@@ -7,11 +7,11 @@
 
 buildPythonPackage rec {
   pname = "soco";
-  version = "0.15";
+  version = "0.16";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "18bxpbd7l9gns0jpvx09z023kbbz7b6i4f99i8silsb1jv682kg0";
+    sha256 = "7bed4475e3f134283af1f520a9b2e6ce2a8e69bdc1b58ee68528b3d093972424";
   };
 
   propagatedBuildInputs = [ xmltodict requests ];
diff --git a/pkgs/development/python-modules/spglib/default.nix b/pkgs/development/python-modules/spglib/default.nix
index 9b51c445e73..7385387eb86 100644
--- a/pkgs/development/python-modules/spglib/default.nix
+++ b/pkgs/development/python-modules/spglib/default.nix
@@ -2,11 +2,11 @@
 
 buildPythonPackage rec {
   pname = "spglib";
-  version = "1.10.4.1";
+  version = "1.10.4.11";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "1a50c48dfea450c431a6d6790aa2ebbb10dc43eef97f2794f5038ed1eeecbd30";
+    sha256 = "13b0a227d2dc4079fe36d5bcce4e672400c7c5dfc5d3cd25ccb9521ef592d93e";
   };
 
   propagatedBuildInputs = [ numpy ];
diff --git a/pkgs/development/python-modules/sphinx/default.nix b/pkgs/development/python-modules/sphinx/default.nix
index 97f76be15cb..9e71766065c 100644
--- a/pkgs/development/python-modules/sphinx/default.nix
+++ b/pkgs/development/python-modules/sphinx/default.nix
@@ -26,10 +26,10 @@
 
 buildPythonPackage rec {
   pname = "Sphinx";
-  version = "1.7.6";
+  version = "1.7.8";
   src = fetchPypi {
     inherit pname version;
-    sha256 = "217ad9ece2156ed9f8af12b5d2c82a499ddf2c70a33c5f81864a08d8c67b9efc";
+    sha256 = "a07050845cc9a2f4026a6035cc8ed795a5ce7be6528bbc82032385c10807dfe7";
   };
   LC_ALL = "en_US.UTF-8";
 
diff --git a/pkgs/development/python-modules/sqlalchemy/default.nix b/pkgs/development/python-modules/sqlalchemy/default.nix
index 8c3c6fe2374..2f755869d79 100644
--- a/pkgs/development/python-modules/sqlalchemy/default.nix
+++ b/pkgs/development/python-modules/sqlalchemy/default.nix
@@ -9,11 +9,11 @@
 
 buildPythonPackage rec {
   pname = "SQLAlchemy";
-  version = "1.2.10";
+  version = "1.2.11";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "72325e67fb85f6e9ad304c603d83626d1df684fdf0c7ab1f0352e71feeab69d8";
+    sha256 = "ef6569ad403520ee13e180e1bfd6ed71a0254192a934ec1dbd3dbf48f4aa9524";
   };
 
   checkInputs = [
diff --git a/pkgs/development/python-modules/sqlmap/default.nix b/pkgs/development/python-modules/sqlmap/default.nix
index 674d1e66f7e..5713d7591dc 100644
--- a/pkgs/development/python-modules/sqlmap/default.nix
+++ b/pkgs/development/python-modules/sqlmap/default.nix
@@ -5,11 +5,11 @@
 
 buildPythonPackage rec {
   pname = "sqlmap";
-  version = "1.2.7";
+  version = "1.2.8";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "9e570fcac05b3231d5e01398e496b88a78601938bba228e381994a1b3fe3bd88";
+    sha256 = "d261d93e7abed20543c261327d30b9f9936f0bed3c1a595f39218eeb66094526";
   };
 
   # No tests in archive
diff --git a/pkgs/development/python-modules/statistics/default.nix b/pkgs/development/python-modules/statistics/default.nix
new file mode 100644
index 00000000000..4380e592ff5
--- /dev/null
+++ b/pkgs/development/python-modules/statistics/default.nix
@@ -0,0 +1,27 @@
+{ lib
+, fetchPypi
+, buildPythonPackage
+, docutils
+}:
+
+buildPythonPackage rec {
+  pname = "statistics";
+  version = "1.0.3.5";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "2dc379b80b07bf2ddd5488cad06b2b9531da4dd31edb04dc9ec0dc226486c138";
+  };
+
+  propagatedBuildInputs = [ docutils ];
+
+  # statistics package does not have any tests
+  doCheck = false;
+
+  meta = {
+    description = "A Python 2.* port of 3.4 Statistics Module";
+    homepage = https://github.com/digitalemagine/py-statistics;
+    license = lib.licenses.asl20;
+    maintainers = with lib.maintainers; [ costrouc ];
+  };
+}
diff --git a/pkgs/development/python-modules/stripe/default.nix b/pkgs/development/python-modules/stripe/default.nix
index f2e4b946b5d..c1ebdec90cc 100644
--- a/pkgs/development/python-modules/stripe/default.nix
+++ b/pkgs/development/python-modules/stripe/default.nix
@@ -3,7 +3,7 @@
 
 buildPythonPackage rec {
   pname = "stripe";
-  version = "2.0.3";
+  version = "2.6.0";
 
   # Tests require network connectivity and there's no easy way to disable
   # them. ~ C.
@@ -11,7 +11,7 @@ buildPythonPackage rec {
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "17a618541c19a48d5591f4011a282cbcbbe2d05c361109f8f5381aeec05eb270";
+    sha256 = "ce8fc8af33e12d3d92b083b86952227e9af6854eaf6a044a7725ac543b0582f8";
   };
 
   checkInputs = [ unittest2 mock ];
diff --git a/pkgs/development/python-modules/svg-path/default.nix b/pkgs/development/python-modules/svg-path/default.nix
index 04031fcbc10..3a11bf67e13 100644
--- a/pkgs/development/python-modules/svg-path/default.nix
+++ b/pkgs/development/python-modules/svg-path/default.nix
@@ -1,11 +1,11 @@
 { stdenv, buildPythonPackage, fetchPypi }:
 buildPythonPackage rec {
   pname = "svg.path";
-  version = "2.2";
+  version = "3.0";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "08kp03i4yiqdkz7a7l7d7kzszahmhigrml2502zi1ybndrh7ayxw";
+    sha256 = "7b568f90f67fd25413c8da9f8bc9f9f8ab089425c20fa03330e97e77d13880ee";
   };
 
   meta = with stdenv.lib; {
diff --git a/pkgs/development/python-modules/sybil/default.nix b/pkgs/development/python-modules/sybil/default.nix
index 6930cb2a559..c78016d7296 100644
--- a/pkgs/development/python-modules/sybil/default.nix
+++ b/pkgs/development/python-modules/sybil/default.nix
@@ -3,11 +3,11 @@
 
 buildPythonApplication rec {
   pname   = "sybil";
-  version = "1.0.8";
+  version = "1.0.9";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "1e17e10bac4c56ef5b6752866a7d100f5ae856ff97d805c4d6cac73be80863d3";
+    sha256 = "41d2f1dba8fd1d8ead5e9b1220b590fab8b0d1ca01d43da08555b1fb08d4d8e8";
   };
 
   checkInputs = [ pytest nose ];
diff --git a/pkgs/development/python-modules/tox/default.nix b/pkgs/development/python-modules/tox/default.nix
index 7719687f2ea..1cb9770367a 100644
--- a/pkgs/development/python-modules/tox/default.nix
+++ b/pkgs/development/python-modules/tox/default.nix
@@ -11,7 +11,7 @@
 
 buildPythonPackage rec {
   pname = "tox";
-  version = "3.1.2";
+  version = "3.2.1";
 
   buildInputs = [ setuptools_scm ];
   propagatedBuildInputs = [ packaging pluggy py six virtualenv ];
@@ -20,7 +20,7 @@ buildPythonPackage rec {
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "9f0cbcc36e08c2c4ae90d02d3d1f9a62231f974bcbc1df85e8045946d8261059";
+    sha256 = "eb61aa5bcce65325538686f09848f04ef679b5cd9b83cc491272099b28739600";
   };
 
   meta = with lib; {
diff --git a/pkgs/development/python-modules/tqdm/default.nix b/pkgs/development/python-modules/tqdm/default.nix
index fd5cd47be38..5b65e156a42 100644
--- a/pkgs/development/python-modules/tqdm/default.nix
+++ b/pkgs/development/python-modules/tqdm/default.nix
@@ -10,11 +10,11 @@
 
 buildPythonPackage rec {
   pname = "tqdm";
-  version = "4.23.4";
+  version = "4.25.0";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "77b8424d41b31e68f437c6dd9cd567aebc9a860507cb42fbd880a5f822d966fe";
+    sha256 = "a3364bd83ce4777320b862e3c8a93d7da91e20a95f06ef79bed7dd71c654cafa";
   };
 
   buildInputs = [ nose coverage glibcLocales flake8 ];
diff --git a/pkgs/development/python-modules/trio/default.nix b/pkgs/development/python-modules/trio/default.nix
index c630668386e..4924fa527c6 100644
--- a/pkgs/development/python-modules/trio/default.nix
+++ b/pkgs/development/python-modules/trio/default.nix
@@ -12,12 +12,12 @@
 
 buildPythonPackage rec {
   pname = "trio";
-  version = "0.5.0";
+  version = "0.6.0";
   disabled = pythonOlder "3.5";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "ce0b4f59e2f41af0433247f92ce83116bf356a3c2ab5ca5942cf359a1105b4a8";
+    sha256 = "7a80c10b89068950aa649edd4b09a6f56236642c2c2e648b956289d2301fdb9e";
   };
 
   checkInputs = [ pytest pyopenssl trustme ];
diff --git a/pkgs/development/python-modules/txaio/default.nix b/pkgs/development/python-modules/txaio/default.nix
index 5558a7e339a..2bfdbae918a 100644
--- a/pkgs/development/python-modules/txaio/default.nix
+++ b/pkgs/development/python-modules/txaio/default.nix
@@ -2,11 +2,11 @@
 
 buildPythonPackage rec {
   pname = "txaio";
-  version = "2.10.0";
+  version = "18.7.1";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "4797f9f6a9866fe887c96abc0110a226dd5744c894dc3630870542597ad30853";
+    sha256 = "701de939e90bb80f7e085357081552437526752199def5541dddfc34c0b0593f";
   };
 
   checkInputs = [ pytest mock ];
diff --git a/pkgs/development/python-modules/typeguard/default.nix b/pkgs/development/python-modules/typeguard/default.nix
index a6eb75b53cf..6ccde34f48a 100644
--- a/pkgs/development/python-modules/typeguard/default.nix
+++ b/pkgs/development/python-modules/typeguard/default.nix
@@ -8,11 +8,11 @@
 
 buildPythonPackage rec {
   pname = "typeguard";
-  version = "2.2.0";
+  version = "2.2.2";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "e588ff78b7093fc31c3b00c78db09b9b3764157b03b867f25ccd1dd3efd96ffb";
+    sha256 = "b8ddc6e2e60bd64b7003f9a685a09ba387b74adf2f6bea7534a76d61892f573e";
   };
 
   buildInputs = [ setuptools_scm ];
diff --git a/pkgs/development/python-modules/typing/default.nix b/pkgs/development/python-modules/typing/default.nix
index d1a9185d5a1..e363ca22cf2 100644
--- a/pkgs/development/python-modules/typing/default.nix
+++ b/pkgs/development/python-modules/typing/default.nix
@@ -5,11 +5,11 @@ let
 
 in buildPythonPackage rec {
   pname = "typing";
-  version = "3.6.4";
+  version = "3.6.6";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "d400a9344254803a2368533e4533a4200d21eb7b6b729c173bc38201a74db3f2";
+    sha256 = "4027c5f6127a6267a435201981ba156de91ad0d1d98e9ddc2aa173453453492d";
   };
 
   # Error for Python3.6: ImportError: cannot import name 'ann_module'
diff --git a/pkgs/development/python-modules/uproot/default.nix b/pkgs/development/python-modules/uproot/default.nix
index 368f787313b..e2cc1105f09 100644
--- a/pkgs/development/python-modules/uproot/default.nix
+++ b/pkgs/development/python-modules/uproot/default.nix
@@ -2,11 +2,11 @@
 
 buildPythonPackage rec {
   pname = "uproot";
-  version = "2.9.6";
+  version = "2.9.11";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "1fb8dd19bd1f1ed376a96e92b32ff44f7d3688bda55eda9055898111fdac8391";
+    sha256 = "da71e9e239129ec2ae7a62f9d35aebd46456f05e000ef14f32fe2c9fa8ec92c2";
   };
 
   propagatedBuildInputs = [
diff --git a/pkgs/development/python-modules/vega/default.nix b/pkgs/development/python-modules/vega/default.nix
index 1813ae587c1..09106e3a6d4 100644
--- a/pkgs/development/python-modules/vega/default.nix
+++ b/pkgs/development/python-modules/vega/default.nix
@@ -3,11 +3,11 @@
 
 buildPythonPackage rec {
   pname = "vega";
-  version = "1.3.0";
+  version = "1.4.0";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "2c5561238fbd4a0669aea457decb47c5155e9741b47a41f23cc030387f725edc";
+    sha256 = "cf9701dac0111c09ea009ab06cbb81f27b1d9c23ebf58ebdf08b6994a37f13ac";
   };
 
   buildInputs = [ pytest ];
diff --git a/pkgs/development/python-modules/voluptuous/default.nix b/pkgs/development/python-modules/voluptuous/default.nix
index 0d4f250509f..b45a46b3a83 100644
--- a/pkgs/development/python-modules/voluptuous/default.nix
+++ b/pkgs/development/python-modules/voluptuous/default.nix
@@ -2,11 +2,11 @@
 
 buildPythonPackage rec {
   pname = "voluptuous";
-  version = "0.11.1";
+  version = "0.11.5";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "af7315c9fa99e0bfd195a21106c82c81619b42f0bd9b6e287b797c6b6b6a9918";
+    sha256 = "567a56286ef82a9d7ae0628c5842f65f516abcb496e74f3f59f1d7b28df314ef";
   };
 
   checkInputs = [ nose ];
diff --git a/pkgs/development/python-modules/websockets_client/default.nix b/pkgs/development/python-modules/websockets_client/default.nix
index 846e9a2a0f5..194f3f126a3 100644
--- a/pkgs/development/python-modules/websockets_client/default.nix
+++ b/pkgs/development/python-modules/websockets_client/default.nix
@@ -1,11 +1,11 @@
 { stdenv, buildPythonPackage, fetchPypi, six }:
 buildPythonPackage rec {
   pname = "websocket_client";
-  version = "0.48.0";
+  version = "0.51.0";
 
   src = fetchPypi {
     inherit version pname;
-    sha256 = "18f1170e6a1b5463986739d9fd45c4308b0d025c1b2f9b88788d8f69e8a5eb4a";
+    sha256 = "030bbfbf29ac9e315ffb207ed5ed42b6981b5038ea00d1e13b02b872cc95e8f6";
   };
 
   prePatch = ''
diff --git a/pkgs/development/python-modules/whitenoise/default.nix b/pkgs/development/python-modules/whitenoise/default.nix
index d2359b2195f..007bb9c879b 100644
--- a/pkgs/development/python-modules/whitenoise/default.nix
+++ b/pkgs/development/python-modules/whitenoise/default.nix
@@ -2,11 +2,11 @@
 
 buildPythonPackage rec {
   pname = "whitenoise";
-  version = "4.0b4";
+  version = "4.0";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "0ra2bbsihwfhnf1ibahzzabgfjfghxqcrbfx6r5r50mlil5n8bf4";
+    sha256 = "1e206c5adfb849942ddd057e599ac472ec1a85d56ae78a5ba24f243ea46a89c5";
   };
 
   # No tests
diff --git a/pkgs/development/python-modules/widgetsnbextension/default.nix b/pkgs/development/python-modules/widgetsnbextension/default.nix
index 0f102dda106..db992c7b932 100644
--- a/pkgs/development/python-modules/widgetsnbextension/default.nix
+++ b/pkgs/development/python-modules/widgetsnbextension/default.nix
@@ -7,11 +7,11 @@
 
 buildPythonPackage rec {
   pname = "widgetsnbextension";
-  version = "3.3.0";
+  version = "3.4.0";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "c5280a62d293735cdadc7b8884e2affcfb0488420ee09963577f042359726392";
+    sha256 = "c9d6e426a1d79d132b57b93b368feba2c66eb7b0fd34bdb901716b4b88e94497";
   };
 
   propagatedBuildInputs = [ notebook ];
diff --git a/pkgs/development/python-modules/zeep/default.nix b/pkgs/development/python-modules/zeep/default.nix
index b14e0226d73..09beb9d8991 100644
--- a/pkgs/development/python-modules/zeep/default.nix
+++ b/pkgs/development/python-modules/zeep/default.nix
@@ -25,11 +25,11 @@
 
 buildPythonPackage rec {
   pname = "zeep";
-  version = "3.0.0";
+  version = "3.1.0";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "faab59d57275ce35845f42371cca83b3957982cdca9621228153fb99c770c4fc";
+    sha256 = "b2d96881689c3f29e8ea5c8c6abb2b17fb0f470deee15d0d7bec4e74592850f6";
   };
 
   propagatedBuildInputs = [
diff --git a/pkgs/development/python-modules/zodbpickle/default.nix b/pkgs/development/python-modules/zodbpickle/default.nix
index c3f41d281c6..746099368fb 100644
--- a/pkgs/development/python-modules/zodbpickle/default.nix
+++ b/pkgs/development/python-modules/zodbpickle/default.nix
@@ -5,12 +5,12 @@
 
 buildPythonPackage rec {
   pname = "zodbpickle";
-  version = "1.0.1";
+  version = "1.0.2";
   disabled = isPyPy; # https://github.com/zopefoundation/zodbpickle/issues/10
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "5fdfa84f05b25511a4e1190ec98728aa487e2eb6db016a951fdbb79bcc7307e0";
+    sha256 = "f26e6eba6550ff1575ef2f2831fc8bc0b465f17f9757d0b6c7db55fab5702061";
   };
 
   # fails..
diff --git a/pkgs/tools/admin/awscli/default.nix b/pkgs/tools/admin/awscli/default.nix
index c454cca0ed6..ccd9f05a335 100644
--- a/pkgs/tools/admin/awscli/default.nix
+++ b/pkgs/tools/admin/awscli/default.nix
@@ -44,7 +44,7 @@ in py.pkgs.buildPythonApplication rec {
 
   postPatch = ''
     for i in {py,cfg}; do
-      substituteInPlace setup.$i --replace "botocore==1.10.10" "botocore>=1.10.9,<=1.11"
+      substituteInPlace setup.$i --replace "botocore==1.10.65" "botocore>=1.10.9,<=1.11"
     done
   '';
 
diff --git a/pkgs/tools/filesystems/e2fsprogs/default.nix b/pkgs/tools/filesystems/e2fsprogs/default.nix
index 0e983ca219b..d5f43e31702 100644
--- a/pkgs/tools/filesystems/e2fsprogs/default.nix
+++ b/pkgs/tools/filesystems/e2fsprogs/default.nix
@@ -1,11 +1,11 @@
 { stdenv, buildPackages, fetchurl, pkgconfig, libuuid, gettext, texinfo, perl }:
 
 stdenv.mkDerivation rec {
-  name = "e2fsprogs-1.44.3";
+  name = "e2fsprogs-1.44.4";
 
   src = fetchurl {
     url = "mirror://sourceforge/e2fsprogs/${name}.tar.gz";
-    sha256 = "1gl34i2dy1n7aky9g0jgdybl3ar2zh8i8xnghrcbb5pvws66vbn2";
+    sha256 = "1cnwfmv9r7s73xhgghqspjq593pc4qghh80wjd0kjdgwy247cw6x";
   };
 
   outputs = [ "bin" "dev" "out" "man" "info" ];
diff --git a/pkgs/tools/misc/hdf5/default.nix b/pkgs/tools/misc/hdf5/default.nix
index 31813c0b880..e481a31e926 100644
--- a/pkgs/tools/misc/hdf5/default.nix
+++ b/pkgs/tools/misc/hdf5/default.nix
@@ -16,11 +16,11 @@ assert !cpp || mpi == null;
 let inherit (stdenv.lib) optional optionals; in
 
 stdenv.mkDerivation rec {
-  version = "1.10.2";
+  version = "1.10.3";
   name = "hdf5-${version}";
   src = fetchurl {
     url = "https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.10/${name}/src/${name}.tar.bz2";
-    sha256 = "0wfb3w6dzi6zr2g1sdswqy9lxbp7yr4blvyi7k2xya7izmxmpb8w";
+    sha256 = "1a85v6812afi6k3gmfdcj80f6ys9kc80v7ysz39pz9948z7dqp66";
  };
 
   passthru = {
diff --git a/pkgs/tools/networking/modem-manager/default.nix b/pkgs/tools/networking/modem-manager/default.nix
index 8612808687e..6ca8c892562 100644
--- a/pkgs/tools/networking/modem-manager/default.nix
+++ b/pkgs/tools/networking/modem-manager/default.nix
@@ -1,4 +1,4 @@
-{ stdenv, fetchurl, udev, libgudev, polkit, dbus-glib, ppp, gettext, pkgconfig
+{ stdenv, fetchurl, glib, udev, libgudev, polkit, ppp, gettext, pkgconfig
 , libmbim, libqmi, systemd, fetchpatch }:
 
 stdenv.mkDerivation rec {
@@ -13,7 +13,7 @@ stdenv.mkDerivation rec {
 
   nativeBuildInputs = [ gettext pkgconfig ];
 
-  buildInputs = [ udev libgudev polkit dbus-glib ppp libmbim libqmi systemd ];
+  buildInputs = [ glib udev libgudev polkit ppp libmbim libqmi systemd ];
 
   patches = [
     # Patch dependency on glib headers, this breaks packages using core headers (networkmanager-qt)
diff --git a/pkgs/tools/virtualization/awsebcli/default.nix b/pkgs/tools/virtualization/awsebcli/default.nix
index b55ac457305..b1693bd262f 100644
--- a/pkgs/tools/virtualization/awsebcli/default.nix
+++ b/pkgs/tools/virtualization/awsebcli/default.nix
@@ -1,7 +1,7 @@
-{ stdenv, python }:
+{ stdenv, python3, glibcLocales }:
 let
 
-  localPython = python.override {
+  localPython = python3.override {
     packageOverrides = self: super: {
       cement = super.cement.overridePythonAttrs (oldAttrs: rec {
         version = "2.8.2";
@@ -61,6 +61,12 @@ in with localPython.pkgs; buildPythonApplication rec {
     sha256 = "128dgxyz2bgl3r4jdkbmjs280004bm0dwzln7p6ly3yjs2x37jl6";
   };
 
+  buildInputs = [
+    glibcLocales
+  ];
+
+  LC_ALL = "en_US.UTF-8";
+
   checkInputs = [
     pytest mock nose pathspec colorama requests docutils
   ];
diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix
index f3679f497d5..c21a0c41eba 100644
--- a/pkgs/top-level/all-packages.nix
+++ b/pkgs/top-level/all-packages.nix
@@ -4491,6 +4491,8 @@ with pkgs;
 
   padthv1 = callPackage ../applications/audio/padthv1 { };
 
+  pagmo2 = callPackage ../development/libraries/pagmo2 { };
+
   pakcs = callPackage ../development/compilers/pakcs {};
 
   pal = callPackage ../tools/misc/pal { };
@@ -8831,7 +8833,7 @@ with pkgs;
 
   grabserial = callPackage ../development/tools/grabserial { };
 
-  mypy = python3Packages.mypy;
+  mypy = with python3Packages; toPythonApplication mypy;
 
   ### DEVELOPMENT / LIBRARIES
 
diff --git a/pkgs/top-level/perl-packages.nix b/pkgs/top-level/perl-packages.nix
index 3623e751123..51d1a1c2215 100644
--- a/pkgs/top-level/perl-packages.nix
+++ b/pkgs/top-level/perl-packages.nix
@@ -133,7 +133,7 @@ let
       url = "mirror://cpan/authors/id/M/MD/MDOOTSON/${name}.tar.gz";
       sha256 = "0jg2dmkzhj03f6b0vmv597yryfw9cclsdn9ynvvlrzzgpd5lw8jk";
     };
-    propagatedBuildInputs = [ pkgs.pkgconfig pkgs.gtk2 pkgs.wxGTK ModulePluggable ];
+    propagatedBuildInputs = [ pkgs.pkgconfig pkgs.gtk2 pkgs.wxGTK30 ModulePluggable ];
     buildInputs = [ LWPProtocolHttps ];
   };
 
@@ -215,7 +215,7 @@ let
       url = "mirror://cpan/authors/id/M/MS/MSCHOUT/${name}.tar.gz";
       sha256 = "58daeb3e44c681ff88f8fb00e4aabaa7a40cbee73dbdb84fcf6c285b15d357bd";
     };
-    buildInputs = [ ApacheTest URI ];
+    buildInputs = [ ApacheTest ];
     propagatedBuildInputs = [ ClassLoad HTTPBody HashMultiValue WWWFormUrlEncoded ];
 
     # Fails because /etc/protocols is not available in sandbox and make
@@ -526,10 +526,10 @@ let
   };
 
   ArchiveZip = buildPerlPackage {
-    name = "Archive-Zip-1.60";
+    name = "Archive-Zip-1.62";
     src = fetchurl {
-      url = mirror://cpan/authors/id/P/PH/PHRED/Archive-Zip-1.60.tar.gz;
-      sha256 = "02y2ylq83hy9kgj57sc0239x65br9sm98c0chsm61s08yc2mpiza";
+      url = mirror://cpan/authors/id/P/PH/PHRED/Archive-Zip-1.62.tar.gz;
+      sha256 = "1jax173w7nm5r6k7ymfcskvs1rw590lyscbqrnfbkjj4cxc65wrb";
     };
     buildInputs = [ TestMockModule ];
     meta = {
@@ -1094,10 +1094,10 @@ let
   };
 
   CarpAlways = buildPerlPackage rec {
-    name = "Carp-Always-0.13";
+    name = "Carp-Always-0.16";
     src = fetchurl {
       url = "mirror://cpan/authors/id/F/FE/FERREIRA/${name}.tar.gz";
-      sha256 = "0i2rifkr7ybfcdsqana52487z7vxp2l5qdra0f6ik0ddhn6rzii1";
+      sha256 = "1wb6b0qjga7kvn4p8df6k4g1pl2yzaqiln1713xidh3i454i3alq";
     };
     meta = {
       description = "Warns and dies noisily with stack backtraces";
@@ -1742,10 +1742,10 @@ let
   };
 
   CGI = buildPerlPackage rec {
-    name = "CGI-4.38";
+    name = "CGI-4.40";
     src = fetchurl {
       url = "mirror://cpan/authors/id/L/LE/LEEJO/${name}.tar.gz";
-      sha256 = "8c58f4a529bb92a914b22b7e64c5e31185c9854a4070a6dfad44fe5cc248e7d4";
+      sha256 = "10efff3061b3c31a33b3cc59f955aef9c88d57d12dbac46389758cef92f24f56";
     };
     buildInputs = [ TestDeep TestNoWarnings TestWarn ];
     propagatedBuildInputs = [ HTMLParser ];
@@ -1854,10 +1854,10 @@ let
   };
 
   CGISimple = buildPerlModule rec {
-    name = "CGI-Simple-1.15";
+    name = "CGI-Simple-1.16";
     src = fetchurl {
-      url = mirror://cpan/authors/id/M/MA/MANWAR/CGI-Simple-1.15.tar.gz;
-      sha256 = "013dcy9k4sj9alkksk5aqz65ryxw0rxgg71c7w666y941gd8n46q";
+      url = mirror://cpan/authors/id/M/MA/MANWAR/CGI-Simple-1.16.tar.gz;
+      sha256 = "1j07qy22a9k4g1xasxma7yzfmwwn3iy50rkxdhz8hz9f09hiym0f";
     };
     propagatedBuildInputs = [ IOStringy ];
     meta = {
@@ -2741,10 +2741,10 @@ let
   };
 
   Coro = buildPerlPackage rec {
-     name = "Coro-6.514";
+     name = "Coro-6.52";
      src = fetchurl {
-       url = mirror://cpan/authors/id/M/ML/MLEHMANN/Coro-6.514.tar.gz;
-       sha256 = "0qndvq74knyra9r98pyllsxz0s80dzc1ljx10arjv9whja1l6cyq";
+       url = mirror://cpan/authors/id/M/ML/MLEHMANN/Coro-6.52.tar.gz;
+       sha256 = "1q744smw6m676v8n0ww8jvmh1zg1iw7f7clzblwbfgmhy03h5ja9";
      };
      propagatedBuildInputs = [ AnyEvent Guard commonsense ];
      buildInputs = [ CanaryStability ];
@@ -2781,10 +2781,10 @@ let
   };
 
   CpanelJSONXS = buildPerlPackage rec {
-    name = "Cpanel-JSON-XS-4.04";
+    name = "Cpanel-JSON-XS-4.05";
     src = fetchurl {
       url = "mirror://cpan/authors/id/R/RU/RURBAN/${name}.tar.gz";
-      sha256 = "e128702a266b9a690bd3d380f726c229f9d6d795e8e206b9d32309d06825b2cd";
+      sha256 = "dd2b69265604ac6f18b47131565f712d55ed8df3b85f8f58f0c98cad17383663";
     };
     meta = {
       description = "CPanel fork of JSON::XS, fast and correct serializing";
@@ -2871,10 +2871,10 @@ let
   };
 
   CPANPerlReleases = buildPerlPackage rec {
-    name = "CPAN-Perl-Releases-3.70";
+    name = "CPAN-Perl-Releases-3.74";
     src = fetchurl {
       url = "mirror://cpan/authors/id/B/BI/BINGOS/${name}.tar.gz";
-      sha256 = "1yv9gq3rzhccskmpd9nn2n8v8zc6r9rlq5x47l0yva29yfgqb16r";
+      sha256 = "0qdh79fl38cyq9kp2g2s934gl1nn5jd88rgmqarqcmja8xhpfcp3";
     };
     meta = {
       homepage = https://github.com/bingos/cpan-perl-releases;
@@ -3657,10 +3657,10 @@ let
   };
 
   DateTime = buildPerlPackage rec {
-    name = "DateTime-1.49";
+    name = "DateTime-1.50";
     src = fetchurl {
       url = "mirror://cpan/authors/id/D/DR/DROLSKY/${name}.tar.gz";
-      sha256 = "0hbw4zq1562slnz7g7hyhfhyq98dzkk3i5g21x3xra5cvfix93kh";
+      sha256 = "165iqk1xvhs5j0kzsipa7aqycx3h37wqsl2r4jl104yqvmqhqszd";
     };
     buildInputs = [ CPANMetaCheck TestFatal TestWarnings ];
     propagatedBuildInputs = [ DateTimeLocale DateTimeTimeZone ];
@@ -5950,10 +5950,10 @@ let
   };
 
   FileMimeInfo = buildPerlPackage rec {
-    name = "File-MimeInfo-0.28";
+    name = "File-MimeInfo-0.29";
     src = fetchurl {
-      url = mirror://cpan/authors/id/M/MI/MICHIELB/File-MimeInfo-0.28.tar.gz;
-      sha256 = "1ipbh63bkh1r2gy5g7q4bzhki8j29mm1jkhbv60p9vwsdys5s91a";
+      url = mirror://cpan/authors/id/M/MI/MICHIELB/File-MimeInfo-0.29.tar.gz;
+      sha256 = "1sh8r6vczyz08zm8vfsjmkg6a165wch54akjdrd1vbifcmwjg5pi";
     };
     doCheck = false; # Failed test 'desktop file is the right one'
     buildInputs = [ FileBaseDir FileDesktopEntry ];
@@ -6269,10 +6269,10 @@ let
   };
 
   Filter = buildPerlPackage {
-    name = "Filter-1.58";
+    name = "Filter-1.59";
     src = fetchurl {
-      url = mirror://cpan/authors/id/R/RU/RURBAN/Filter-1.58.tar.gz;
-      sha256 = "6de91cb4cbfe08d0ccffbca39aed57f9237be602b8183f13fd163fc8cb657f3d";
+      url = mirror://cpan/authors/id/R/RU/RURBAN/Filter-1.59.tar.gz;
+      sha256 = "b4babfad4e0566a9a61199735f6e622a60d3274122752304f18f623412bf4e5a";
     };
     meta = {
       description = "Source Filters";
@@ -6367,10 +6367,10 @@ let
   };
 
   GamesSolitaireVerify = buildPerlModule {
-    name = "Games-Solitaire-Verify-0.1800";
+    name = "Games-Solitaire-Verify-0.1900";
     src = fetchurl {
-      url = mirror://cpan/authors/id/S/SH/SHLOMIF/Games-Solitaire-Verify-0.1800.tar.gz;
-      sha256 = "935ba997c49437a095adb39fd18233d5e378941aa9974df46e56aa6234f1fced";
+      url = mirror://cpan/authors/id/S/SH/SHLOMIF/Games-Solitaire-Verify-0.1900.tar.gz;
+      sha256 = "6b17847bd69da05ee089562cf40f2aac15e64c113175eca4fb501d4e86b48181";
     };
     buildInputs = [ TestDifferences ];
     propagatedBuildInputs = [ ClassXSAccessor ExceptionClass ListMoreUtils ];
@@ -6465,10 +6465,10 @@ let
   };
 
   GetoptLongDescriptive = buildPerlPackage rec {
-    name = "Getopt-Long-Descriptive-0.102";
+    name = "Getopt-Long-Descriptive-0.103";
     src = fetchurl {
       url = "mirror://cpan/authors/id/R/RJ/RJBS/${name}.tar.gz";
-      sha256 = "9ad4b98f294aa0515cc3150a1ae878d39e470762b78d8bd9df055eba9dea2846";
+      sha256 = "70e1bae7404a9dfb638b5d12e5bd4ea97e3bee743a4555909307d68e0111f4b2";
     };
     buildInputs = [ CPANMetaCheck TestFatal TestWarnings ];
     propagatedBuildInputs = [ ParamsValidate SubExporter ];
@@ -7795,10 +7795,10 @@ let
   };
 
   IOSocketSSL = buildPerlPackage rec {
-    name = "IO-Socket-SSL-2.058";
+    name = "IO-Socket-SSL-2.059";
     src = fetchurl {
       url = "mirror://cpan/authors/id/S/SU/SULLR/${name}.tar.gz";
-      sha256 = "746cd17c292cfc206b394497a060b0582d0b06a1040e6bb27e6530d56786e40b";
+      sha256 = "217debbe0a79f0b7c5669978b4d733271998df4497f4718f78456e5f54d64849";
     };
     propagatedBuildInputs = [ NetSSLeay ];
     # Fix path to default certificate store.
@@ -8774,10 +8774,10 @@ let
   };
 
   LogAny = buildPerlPackage rec {
-    name = "Log-Any-1.706";
+    name = "Log-Any-1.707";
     src = fetchurl {
       url = "mirror://cpan/authors/id/P/PR/PREACTION/${name}.tar.gz";
-      sha256 = "3ed0e5a4b7d490ab00624b7f905421239261f1dc976192aad2c0d1509bec08be";
+      sha256 = "74510f8cbee12637462e7c6020c8943d447a1e8e149a256f8168ee47562c65f1";
     };
     # Syslog test fails.
     preCheck = "rm t/syslog.t";
@@ -9555,7 +9555,7 @@ let
     };
   };
 
-  MLDBM = buildPerlPackage rec {
+  MLDBM = buildPerlModule rec {
     name = "MLDBM-2.05";
     src = fetchurl {
       url = "mirror://cpan/authors/id/C/CH/CHORNY/${name}.tar.gz";
@@ -9729,10 +9729,10 @@ let
   };
 
   ModuleCoreList = buildPerlPackage {
-    name = "Module-CoreList-5.20180720";
+    name = "Module-CoreList-5.20180820";
     src = fetchurl {
-      url = mirror://cpan/authors/id/B/BI/BINGOS/Module-CoreList-5.20180720.tar.gz;
-      sha256 = "0l6dyj4m4qgv2yzq3pp0bkvg1j9nh9mcm1p4x3g3j93gkba7whws";
+      url = mirror://cpan/authors/id/B/BI/BINGOS/Module-CoreList-5.20180820.tar.gz;
+      sha256 = "1ccs5mqcfxjv8bax2nfsg11b2vc3sqyapfapxyzrjhaa2fmdn54l";
     };
     meta = {
       homepage = http://dev.perl.org/;
@@ -9952,11 +9952,11 @@ let
     };
   };
 
-  ModuleScanDeps = let version = "1.24"; in buildPerlPackage {
+  ModuleScanDeps = let version = "1.25"; in buildPerlPackage {
     name = "Module-ScanDeps-${version}";
     src = fetchurl {
       url = "mirror://cpan/authors/id/R/RS/RSCHUPP/Module-ScanDeps-${version}.tar.gz";
-      sha256 = "0s6cj90ckhy351gql52ksh4ms1x8piv26iadl09fcpzkx7j0srw9";
+      sha256 = "13280nq0d6zc58mcz3kvs2m85a741czq0fabk69ks1nr4j1w2nl4";
     };
     buildInputs = [ TestRequires ];
     meta = {
@@ -10031,10 +10031,10 @@ let
     };
   };
   Mojolicious = buildPerlPackage rec {
-    name = "Mojolicious-7.88";
+    name = "Mojolicious-7.93";
     src = fetchurl {
       url = "mirror://cpan/authors/id/S/SR/SRI/${name}.tar.gz";
-      sha256 = "4c4c9c05131fcd175cd6370e15d2586baec1a3ec882cb6971e1f5f52b5e0d785";
+      sha256 = "00c30fc566fee0823af0a75bdf4f170531655df14beca6d51f0e453a43aaad5d";
     };
     meta = {
       homepage = https://mojolicious.org/;
@@ -10057,10 +10057,10 @@ let
   };
 
   MonitoringPlugin = buildPerlPackage rec {
-    name = "Monitoring-Plugin-0.39";
+    name = "Monitoring-Plugin-0.40";
     src = fetchurl {
       url = "mirror://cpan/authors/id/N/NI/NIERLEIN/${name}.tar.gz";
-      sha256 = "030cw86j8712z8rn66k935gbilb5rcj3lnk4n53vh1b2phrszvjw";
+      sha256 = "0vr3wwdn3zs246qwi04bqk8jir6l88j5m59jk97hmfyj4xz6pfpq";
     };
     propagatedBuildInputs = [ ClassAccessor ConfigTiny MathCalcUnits ParamsValidate ];
     meta = {
@@ -10493,12 +10493,12 @@ let
   };
 
   MooseXGetopt = buildPerlModule rec {
-    name = "MooseX-Getopt-0.71";
+    name = "MooseX-Getopt-0.72";
     src = fetchurl {
       url = "mirror://cpan/authors/id/E/ET/ETHER/${name}.tar.gz";
-      sha256 = "de18f8ea0a5650cbbdebecb8f4c028f5f951fc5698332f7b8e20c7874902c259";
+      sha256 = "a378411a061ed239554d2b7f86b2b82bf55f600901243a6ec3fd29557d171b2e";
     };
-    buildInputs = [ ModuleBuildTiny MooseXStrictConstructor PathTiny TestDeep TestFatal TestRequires TestTrap TestWarnings ];
+    buildInputs = [ ModuleBuildTiny MooseXStrictConstructor PathTiny TestDeep TestFatal TestNeeds TestTrap TestWarnings ];
     propagatedBuildInputs = [ GetoptLongDescriptive MooseXRoleParameterized ];
     meta = {
       homepage = https://github.com/moose/MooseX-Getopt;
@@ -10923,10 +10923,10 @@ let
   };
 
   Mouse = buildPerlModule rec {
-    name = "Mouse-2.5.4";
+    name = "Mouse-2.5.6";
     src = fetchurl {
-      url = mirror://cpan/authors/id/S/SK/SKAJI/Mouse-v2.5.4.tar.gz;
-      sha256 = "041nm46bxxyi1fd8w69r45k434b6m43va2s06pr3bys6igxic79d";
+      url = mirror://cpan/authors/id/S/SK/SKAJI/Mouse-v2.5.6.tar.gz;
+      sha256 = "1j3048ip691j91rdig6wrlg6i4jdzhszxmz5pi2g7n355rl2w00l";
     };
     buildInputs = [ DevelPPPort ModuleBuildXSUtil TestException TestFatal TestLeakTrace TestOutput TestRequires TryTiny self.version ];
     NIX_CFLAGS_COMPILE = stdenv.lib.optionalString stdenv.isi686 "-fno-stack-protector";
@@ -11208,7 +11208,7 @@ let
       sha256 = "8391696db9e96c374b72984c0bad9c7d1c9f3b4efe68f9ddf429a77548e0e269";
     };
     nativeBuildInputs = [ pkgs.pkgconfig ];
-    buildInputs = [ TestPod TestPodCoverage pkgs.dbus ];
+    buildInputs = [ pkgs.dbus TestPod TestPodCoverage ];
     propagatedBuildInputs = [ XMLTwig ];
     meta = {
       homepage = http://www.freedesktop.org/wiki/Software/dbus;
@@ -11218,10 +11218,10 @@ let
   };
 
   NetDNS = buildPerlPackage rec {
-    name = "Net-DNS-1.16";
+    name = "Net-DNS-1.17";
     src = fetchurl {
       url = "mirror://cpan/authors/id/N/NL/NLNETLABS/${name}.tar.gz";
-      sha256 = "8163eebaf46d1a870b6f596684f345da7c3a7461d7dba2b85f23e02d8982ea37";
+      sha256 = "9a79fd8fea1a708726c18d193ae4437479206ccb20ffa7f0971371e172e2c2e0";
     };
     propagatedBuildInputs = [ DigestHMAC IOSocketIP ];
     makeMakerFlags = "--noonline-tests";
@@ -11348,10 +11348,10 @@ let
   };
 
   NetPing = buildPerlPackage {
-    name = "Net-Ping-2.68";
+    name = "Net-Ping-2.70";
     src = fetchurl {
-      url = mirror://cpan/authors/id/R/RU/RURBAN/Net-Ping-2.68.tar.gz;
-      sha256 = "d01ac2fcdf684c4a23a07104fbb147cfbdbda47fd5b660912124258f29afd7e3";
+      url = mirror://cpan/authors/id/R/RU/RURBAN/Net-Ping-2.70.tar.gz;
+      sha256 = "41400089736f528cfa1196083905d4bbd313c4653a03fab8578cebd5b5b6aa5a";
     };
     meta = {
       description = "Check a remote host for reachability";
@@ -11848,10 +11848,10 @@ let
   };
 
   ParamsValidationCompiler = buildPerlPackage rec {
-     name = "Params-ValidationCompiler-0.27";
+     name = "Params-ValidationCompiler-0.30";
      src = fetchurl {
-       url = mirror://cpan/authors/id/D/DR/DROLSKY/Params-ValidationCompiler-0.27.tar.gz;
-       sha256 = "1cpr188c2xm0kkmdir6slcsgv7v6ibqff4lax8s0whwx6ml9kaah";
+       url = mirror://cpan/authors/id/D/DR/DROLSKY/Params-ValidationCompiler-0.30.tar.gz;
+       sha256 = "1jqn1l4m4i341g14kmjsf3a1kn7vv6z89cix0xjjgr1v70iywnyw";
      };
      propagatedBuildInputs = [ EvalClosure ExceptionClass ];
      buildInputs = [ Specio Test2PluginNoWarnings Test2Suite TestSimple13 TestWithoutModule ];
@@ -11862,10 +11862,10 @@ let
   };
 
   Paranoid = buildPerlPackage rec {
-    name = "Paranoid-2.05";
+    name = "Paranoid-2.06";
     src = fetchurl {
       url = "mirror://cpan/authors/id/C/CO/CORLISS/Paranoid/${name}.tar.gz";
-      sha256 = "583dfa0279733531f360795ad1cf4aa652d537b2b0bbd3c6925d0c8d75cbb3df";
+      sha256 = "48763ec19d0a4194ecf613bd63e46325510228da9100c2e796615dc778612d3c";
     };
     patches = [ ../development/perl-modules/Paranoid-blessed-path.patch ];
     preConfigure = ''
@@ -12000,10 +12000,10 @@ let
   };
 
   PathTiny = buildPerlPackage {
-    name = "Path-Tiny-0.106";
+    name = "Path-Tiny-0.108";
     src = fetchurl {
-      url = mirror://cpan/authors/id/D/DA/DAGOLDEN/Path-Tiny-0.106.tar.gz;
-      sha256 = "308e39087b626013569a15783b896d61916fd1e67d06017f40cff567af36464d";
+      url = mirror://cpan/authors/id/D/DA/DAGOLDEN/Path-Tiny-0.108.tar.gz;
+      sha256 = "3c49482be2b3eb7ddd7e73a5b90cff648393f5d5de334ff126ce7a3632723ff5";
     };
     meta = {
       description = "File path utility";
@@ -12256,10 +12256,10 @@ let
   };
 
   PkgConfig = buildPerlPackage rec {
-    name = "PkgConfig-0.19026";
+    name = "PkgConfig-0.21026";
     src = fetchurl {
       url = "mirror://cpan/authors/id/P/PL/PLICEASE/${name}.tar.gz";
-      sha256 = "5cb6e934d29dd93e04c2fa779f4b7e51361edaf56957b47a232017a4bb7e922c";
+      sha256 = "018f8d3c74e661df66046b26e57f4c5991adafe202af7ea2d1c6f6bcafde584b";
     };
     meta = {
       description = "Pure-Perl Core-Only replacement for pkg-config";
@@ -12566,10 +12566,10 @@ let
   };
 
   PPIxRegexp = buildPerlModule rec {
-    name = "PPIx-Regexp-0.061";
+    name = "PPIx-Regexp-0.062";
     src = fetchurl {
       url = "mirror://cpan/authors/id/W/WY/WYANT/${name}.tar.gz";
-      sha256 = "e2d63a4102024e15994c685672d30c6d708272a1600abcd6241e6f2c1b3b7c92";
+      sha256 = "1218fe4c94b3cb9d894c6cd8a69bb4172eac54ce083b70f7a8bf13868a5a0733";
     };
     propagatedBuildInputs = [ PPI ];
     meta = {
@@ -12678,11 +12678,11 @@ let
   };
 
   ProtocolHTTP2 = buildPerlModule rec {
-    name = "Protocol-HTTP2-1.08";
+    name = "Protocol-HTTP2-1.09";
 
     src = fetchurl {
       url = "mirror://cpan/authors/id/C/CR/CRUX/${name}.tar.gz";
-      sha256 = "06y1djgzbn340hixav85728dvp8mj2mx2qf5fzkqxh145g5q860g";
+      sha256 = "1bc0ybkqhv81dscgzlbr62w4zqjsidcikmkbjanzn83g2b6ia9nc";
     };
     buildInputs = [ AnyEvent ModuleBuildTiny NetSSLeay TestLeakTrace TestSharedFork TestTCP ];
   };
@@ -12946,10 +12946,10 @@ let
   };
 
   PodMarkdown = buildPerlPackage {
-    name = "Pod-Markdown-3.005";
+    name = "Pod-Markdown-3.101";
     src = fetchurl {
-      url = mirror://cpan/authors/id/R/RW/RWSTAUNER/Pod-Markdown-3.005.tar.gz;
-      sha256 = "00s3745kl4vbxqyi2lx149q5ghyfazc4fd00kcpl84bb87jfgdzq";
+      url = mirror://cpan/authors/id/R/RW/RWSTAUNER/Pod-Markdown-3.101.tar.gz;
+      sha256 = "0h7hx4k1c3k00cfnlf226bkxnxaz01705m10vxm9cxh52xn6pzz8";
     };
     buildInputs = [ TestDifferences ];
     meta = {
@@ -13230,7 +13230,7 @@ let
       url = "mirror://cpan/authors/id/K/KK/KKANE/${name}.tar.gz";
       sha256 = "a8652a2214308faff2c68be5ce64c904dcccc5e86be7f32376c1590869d01844";
     };
-    propagatedBuildInputs = [ LWP LWPProtocolhttps URI ];
+    propagatedBuildInputs = [ LWPProtocolHttps ];
     meta = {
       description = "A simple client for interacting with RESTful http/https resources";
       license = with stdenv.lib.licenses; [ artistic1 gpl1Plus ];
@@ -14273,7 +14273,7 @@ let
       url = "mirror://cpan/authors/id/C/CL/CLKAO/${name}.tar.gz";
       sha256 = "1ysgi38zx236cxz539k6d6rw5z0vc70rrglsaf5fk6rnwilw2g6n";
     };
-    propagatedBuildInputs = [ pkgs.subversionClient ];
+    propagatedBuildInputs = [ (pkgs.subversionClient.override { inherit perl; }) ];
   };
 
   Swim = buildPerlPackage rec {
@@ -15851,10 +15851,10 @@ let
   };
 
   TestSimple13 = buildPerlPackage rec {
-    name = "Test-Simple-1.302138";
+    name = "Test-Simple-1.302140";
     src = fetchurl {
-      url = mirror://cpan/authors/id/E/EX/EXODIST/Test-Simple-1.302138.tar.gz;
-      sha256 = "568615a551075d3657cb0cbca55cf3672734c954f0306e9823ecd002aa911655";
+      url = mirror://cpan/authors/id/E/EX/EXODIST/Test-Simple-1.302140.tar.gz;
+      sha256 = "73f5440c7ae55e13706e9ebeaa7247df973226470f028344ea3cd21e1642bd1d";
     };
     meta = {
       description = "Basic utilities for writing tests";
@@ -16203,10 +16203,10 @@ let
   };
 
   TextCSV = buildPerlPackage rec {
-    name = "Text-CSV-1.95";
+    name = "Text-CSV-1.97";
     src = fetchurl {
-      url = mirror://cpan/authors/id/I/IS/ISHIGAKI/Text-CSV-1.95.tar.gz;
-      sha256 = "7e0a11d9c1129a55b68a26aa4b37c894279df255aa63ec8341d514ab848dbf61";
+      url = mirror://cpan/authors/id/I/IS/ISHIGAKI/Text-CSV-1.97.tar.gz;
+      sha256 = "cc350462efa8d39d5c8a1da5f205bc31620cd52d9865a769c8e3ed1b41640fd5";
     };
     meta = {
       description = "Comma-separated values manipulator (using XS or PurePerl)";
@@ -16404,10 +16404,10 @@ let
   };
 
   TextQuoted = buildPerlPackage {
-    name = "Text-Quoted-2.09";
+    name = "Text-Quoted-2.10";
     src = fetchurl {
-      url = mirror://cpan/authors/id/A/AL/ALEXMV/Text-Quoted-2.09.tar.gz;
-      sha256 = "446c3e8da7e65f7988cd36e9da1159614eb0b337d6c4c0dec8f6df7673b96c5f";
+      url = mirror://cpan/authors/id/B/BP/BPS/Text-Quoted-2.10.tar.gz;
+      sha256 = "081bf95ec9220af26cec89161e61bf73f9fbcbfeee1d9af15139e5d7b708f445";
     };
     propagatedBuildInputs = [ TextAutoformat ];
     meta = {
@@ -16456,10 +16456,10 @@ let
   };
 
   TextSimpleTable = buildPerlPackage {
-    name = "Text-SimpleTable-2.05";
+    name = "Text-SimpleTable-2.07";
     src = fetchurl {
-      url = mirror://cpan/authors/id/M/MR/MRAMBERG/Text-SimpleTable-2.05.tar.gz;
-      sha256 = "1akcv3iq4y6mjc88p0j9yvv6g0g5cnc9nvzxnmsswnx5si7v5am5";
+      url = mirror://cpan/authors/id/M/MR/MRAMBERG/Text-SimpleTable-2.07.tar.gz;
+      sha256 = "1v8r8qpzg283p2pqqr8dqrak2bxray1b2jmib0qk75jffqw3yv95";
     };
     meta = {
       description = "Simple eyecandy ASCII tables";
@@ -16997,10 +16997,10 @@ let
   };
 
   TypeTiny = buildPerlPackage {
-    name = "Type-Tiny-1.002002";
+    name = "Type-Tiny-1.004002";
     src = fetchurl {
-      url = mirror://cpan/authors/id/T/TO/TOBYINK/Type-Tiny-1.002002.tar.gz;
-      sha256 = "a85b0c8f99b5c9b5558f0bcc8893b44299fcccf3c264ff924940d09d91d8882c";
+      url = mirror://cpan/authors/id/T/TO/TOBYINK/Type-Tiny-1.004002.tar.gz;
+      sha256 = "e52c7e9593052aed157a15d473b5c25a1dbb3454bf3cd6913df94cc9bb2be707";
     };
     propagatedBuildInputs = [ ExporterTiny ];
     meta = {
@@ -17703,10 +17703,10 @@ let
   };
 
   XMLParserLite = buildPerlPackage {
-    name = "XML-Parser-Lite-0.721";
+    name = "XML-Parser-Lite-0.722";
     src = fetchurl {
-      url = mirror://cpan/authors/id/P/PH/PHRED/XML-Parser-Lite-0.721.tar.gz;
-      sha256 = "1fh8g77nkfv9n07ivilnfxdapx6jx13whf8q0anrmnxrr9pa6qjq";
+      url = mirror://cpan/authors/id/P/PH/PHRED/XML-Parser-Lite-0.722.tar.gz;
+      sha256 = "1vk3jwh1kfcsmc5kvxzqdnb1cllvf0yf27fg0ra0w6jkw4ks143g";
     };
     buildInputs = [ TestRequires ];
     meta = {
@@ -17817,10 +17817,10 @@ let
   };
 
   XMLSemanticDiff = buildPerlModule {
-    name = "XML-SemanticDiff-1.0006";
+    name = "XML-SemanticDiff-1.0007";
     src = fetchurl {
-      url = mirror://cpan/authors/id/S/SH/SHLOMIF/XML-SemanticDiff-1.0006.tar.gz;
-      sha256 = "1z0lkb7xzhw9calz4pbwzry2lqqpy6pw6pvfn2gv70ry1xqycr0k";
+      url = mirror://cpan/authors/id/P/PE/PERIGRIN/XML-SemanticDiff-1.0007.tar.gz;
+      sha256 = "1xd00821y795fy2rag8aizb5wsbbzfxgmdf9qwpvdxn3pgpyzz85";
     };
     propagatedBuildInputs = [ XMLParser ];
     meta = {
diff --git a/pkgs/top-level/python-packages.nix b/pkgs/top-level/python-packages.nix
index b1c5368b188..84472b440a5 100644
--- a/pkgs/top-level/python-packages.nix
+++ b/pkgs/top-level/python-packages.nix
@@ -182,6 +182,8 @@ in {
 
   asana = callPackage ../development/python-modules/asana { };
 
+  ase = callPackage ../development/python-modules/ase { };
+
   asn1crypto = callPackage ../development/python-modules/asn1crypto { };
 
   aspy-yaml = callPackage ../development/python-modules/aspy.yaml { };
@@ -272,6 +274,8 @@ in {
     dbus = pkgs.dbus;
   };
 
+  dftfit = callPackage ../development/python-modules/dftfit { };
+
   discid = callPackage ../development/python-modules/discid { };
 
   discordpy = callPackage ../development/python-modules/discordpy { };
@@ -282,6 +286,8 @@ in {
 
   distorm3 = callPackage ../development/python-modules/distorm3 { };
 
+  docutils = callPackage ../development/python-modules/docutils { };
+
   dogtail = callPackage ../development/python-modules/dogtail { };
 
   diff-match-patch = callPackage ../development/python-modules/diff-match-patch { };
@@ -316,6 +322,10 @@ in {
 
   jira = callPackage ../development/python-modules/jira { };
 
+  lammps-cython = callPackage ../development/python-modules/lammps-cython {
+    mpi = pkgs.openmpi;
+  };
+
   lmtpd = callPackage ../development/python-modules/lmtpd { };
 
   logster = callPackage ../development/python-modules/logster { };
@@ -356,6 +366,8 @@ in {
 
   palettable = callPackage ../development/python-modules/palettable { };
 
+  pathlib = callPackage ../development/python-modules/pathlib { };
+
   pdf2image = callPackage ../development/python-modules/pdf2image { };
 
   pdfminer = callPackage ../development/python-modules/pdfminer_six { };
@@ -400,6 +412,8 @@ in {
 
   PyChromecast = callPackage ../development/python-modules/pychromecast { };
 
+  py-cpuinfo = callPackage ../development/python-modules/py-cpuinfo { };
+
   pydbus = callPackage ../development/python-modules/pydbus { };
 
   pydocstyle = callPackage ../development/python-modules/pydocstyle { };
@@ -416,6 +430,8 @@ in {
 
   pygame_sdl2 = callPackage ../development/python-modules/pygame_sdl2 { };
 
+  pygmo = callPackage ../development/python-modules/pygmo { };
+
   pygobject2 = callPackage ../development/python-modules/pygobject { };
 
   pygobject3 = callPackage ../development/python-modules/pygobject/3.nix { };
@@ -445,6 +461,8 @@ in {
 
   pymatgen = callPackage ../development/python-modules/pymatgen { };
 
+  pymatgen-lammps = callPackage ../development/python-modules/pymatgen-lammps { };
+
   pynisher = callPackage ../development/python-modules/pynisher { };
 
   pyparser = callPackage ../development/python-modules/pyparser { };
@@ -532,6 +550,8 @@ in {
 
   spglib = callPackage ../development/python-modules/spglib { };
 
+  statistics = callPackage ../development/python-modules/statistics { };
+
   sumo = callPackage ../development/python-modules/sumo { };
 
   supervise_api = callPackage ../development/python-modules/supervise_api { };
@@ -1466,7 +1486,7 @@ in {
     '';
   };
 
-  celery = callPackage ../development/python-modules/celery { pytest = self.pytest_32; };
+  celery = callPackage ../development/python-modules/celery { };
 
   cerberus = callPackage ../development/python-modules/cerberus { };
 
@@ -1843,28 +1863,21 @@ in {
     };
   };
 
-  pytest = self.pytest_36;
+  pytest = self.pytest_37;
 
-  pytest_36 = callPackage ../development/python-modules/pytest {
+  pytest_37 = callPackage ../development/python-modules/pytest {
     # hypothesis tests require pytest that causes dependency cycle
     hypothesis = self.hypothesis.override { doCheck = false; };
   };
 
-  # Needed for celery
-  pytest_32 = self.pytest_36.overridePythonAttrs( oldAttrs: rec {
-    version = "3.2.5";
-    src = oldAttrs.src.override {
-      inherit version;
-      sha256 = "6d5bd4f7113b444c55a3bbb5c738a3dd80d43563d063fc42dcb0aaefbdd78b81";
-    };
-  });
-
   pytest-httpbin = callPackage ../development/python-modules/pytest-httpbin { };
 
   pytest-asyncio = callPackage ../development/python-modules/pytest-asyncio { };
 
   pytest-aiohttp = callPackage ../development/python-modules/pytest-aiohttp { };
 
+  pytest-benchmark = callPackage ../development/python-modules/pytest-benchmark { };
+
   pytestcache = callPackage ../development/python-modules/pytestcache { };
 
   pytest-catchlog = callPackage ../development/python-modules/pytest-catchlog { };
@@ -4960,37 +4973,6 @@ in {
     };
   };
 
-
-  docutils = buildPythonPackage rec {
-    name = "docutils-${version}";
-    version = "0.14";
-
-    src = pkgs.fetchurl {
-      url = "mirror://sourceforge/docutils/${name}.tar.gz";
-      sha256 = "0x22fs3pdmr42kvz6c654756wja305qv6cx1zbhwlagvxgr4xrji";
-    };
-
-    checkPhase = if isPy3k then ''
-      ${python.interpreter} test3/alltests.py
-    '' else ''
-      ${python.interpreter} test/alltests.py
-    '';
-
-    # Create symlinks lacking a ".py" suffix, many programs depend on these names
-    postFixup = ''
-      (cd $out/bin && for f in *.py; do
-        ln -s $f $(echo $f | sed -e 's/\.py$//')
-      done)
-    '';
-
-    meta = {
-      description = "An open-source text processing system for processing plaintext documentation into useful formats, such as HTML or LaTeX";
-      homepage = http://docutils.sourceforge.net/;
-      maintainers = with maintainers; [ garbas AndersonTorres ];
-    };
-  };
-
-
   dtopt = buildPythonPackage rec {
     name = "dtopt-0.1";
 
@@ -9415,27 +9397,6 @@ in {
 
   patator = callPackage ../development/python-modules/patator { };
 
-  pathlib = buildPythonPackage rec {
-    name = "pathlib-${version}";
-    version = "1.0.1";
-    disabled = pythonAtLeast "3.4"; # Was added to std library in Python 3.4
-
-    src = pkgs.fetchurl {
-      url = "mirror://pypi/p/pathlib/${name}.tar.gz";
-      sha256 = "17zajiw4mjbkkv6ahp3xf025qglkj0805m9s41c45zryzj6p2h39";
-    };
-
-    checkPhase = ''
-      ${python.interpreter} -m unittest discover
-    '';
-
-    meta = {
-      description = "Object-oriented filesystem paths";
-      homepage = "https://pathlib.readthedocs.org/";
-      license = licenses.mit;
-    };
-  };
-
   pathlib2 = callPackage ../development/python-modules/pathlib2 { };
 
   pathpy = callPackage ../development/python-modules/path.py { };